diff --git a/integration-tests/cli/CHANGELOG.md b/integration-tests/cli/CHANGELOG.md
index 2037b71e0..f22a475d8 100644
--- a/integration-tests/cli/CHANGELOG.md
+++ b/integration-tests/cli/CHANGELOG.md
@@ -1,5 +1,12 @@
 # @openfn/integration-tests-cli
 
+## 1.0.15
+
+### Patch Changes
+
+- Updated dependencies [58a9919]
+  - @openfn/project@0.14.1
+
 ## 1.0.14
 
 ### Patch Changes
diff --git a/integration-tests/cli/package.json b/integration-tests/cli/package.json
index b60284eaa..6ad5957c3 100644
--- a/integration-tests/cli/package.json
+++ b/integration-tests/cli/package.json
@@ -1,7 +1,7 @@
 {
   "name": "@openfn/integration-tests-cli",
   "private": true,
-  "version": "1.0.14",
+  "version": "1.0.15",
   "description": "CLI integration tests",
   "author": "Open Function Group <admin@openfn.org>",
   "license": "ISC",
diff --git a/packages/cli/CHANGELOG.md b/packages/cli/CHANGELOG.md
index f42b3540f..6a71eecbf 100644
--- a/packages/cli/CHANGELOG.md
+++ b/packages/cli/CHANGELOG.md
@@ -1,5 +1,14 @@
 # @openfn/cli
 
+## 1.28.1
+
+### Patch Changes
+
+- 58a9919: Fix an issue where added and removed workflows are ignored by merge
+- 66e7c13: Fix deploy when the target project is a different UUID to the local project
+- Updated dependencies [58a9919]
+  - @openfn/project@0.14.1
+
 ## 1.28.0
 
 ### Minor Changes
diff --git a/packages/cli/package.json b/packages/cli/package.json
index 7fdfd0f05..7863b80b4 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@openfn/cli",
-  "version": "1.28.0",
+  "version": "1.28.1",
   "description": "CLI devtools for the OpenFn toolchain",
   "engines": {
     "node": ">=18",
diff --git a/packages/cli/src/projects/deploy.ts b/packages/cli/src/projects/deploy.ts
index 8e9754679..41a655759 100644
--- a/packages/cli/src/projects/deploy.ts
+++ b/packages/cli/src/projects/deploy.ts
@@ -22,6 +22,8 @@ import type { Provisioner } from '@openfn/lexicon/lightning';
 import type { Logger } from '../util/logger';
 import type { Opts } from '../options';
 
+export const DEFAULT_ENDPOINT = 'https://app.openfn.org';
+
 export type DeployOptions = Pick<
   Opts,
   | 'apiKey'
@@ -33,6 +35,7 @@ export type DeployOptions = Pick<
   | 'logJson'
   | 'confirm'
 > & {
+  project?: string; // this is a CLI positional arg, not an option
   workspace?: string;
   dryRun?: boolean;
   new?: boolean;
@@ -63,7 +66,7 @@ const printProjectName = (project: Project) =>
   `${project.id} (${project.openfn?.uuid || '<no UUID>'})`;
 
 export const command: yargs.CommandModule<DeployOptions> = {
-  command: 'deploy',
+  command: 'deploy [project]',
   aliases: 'push',
   describe: `Deploy the checked out project to a Lightning Instance`,
   builder: (yargs: yargs.Argv<DeployOptions>) =>
@@ -74,7 +77,11 @@ export const command: yargs.CommandModule<DeployOptions> = {
       })
       .example(
         'deploy',
-        'Deploy the checkout project to the connected instance'
+        'Deploy the checked-out project its connected remote instance'
+      )
+      .example(
+        'deploy staging',
+        'Deploy the checkout-out project to the remote project with alias "staging"'
       ),
   handler: ensure('project-deploy', options),
 };
@@ -97,9 +104,11 @@ export const hasRemoteDiverged = (
     if (wf.id in refs) {
       const forkedVersion = refs[wf.id];
       const remoteVersion = remote.getWorkflow(wf.id)?.history.at(-1);
-      if (!versionsEqual(forkedVersion, remoteVersion!)) {
-        diverged ??= [];
-        diverged.push(wf.id);
+      if (remoteVersion) {
+        if (!versionsEqual(forkedVersion, remoteVersion!)) {
+          diverged ??= [];
+          diverged.push(wf.id);
+        }
       }
     } else {
       // TODO what if there's no forked from for this workflow?
@@ -120,26 +129,30 @@ const syncProjects = async (
   config: Required<AuthOptions>,
   ws: Workspace,
   localProject: Project,
+  trackedProject: Project, // the project we want to update
   logger: Logger
 ): Promise<Project> => {
-  logger.info('Attempting to load checked-out project from workspace');
-
   // First step, fetch the latest version and write
   // this may throw!
   let remoteProject: Project;
   try {
+    logger.info('Fetching remote target ', printProjectName(trackedProject));
+    // TODO should we prefer endpoint over alias?
+    // maybe if it's explicitly passed?
+    const endpoint = trackedProject.openfn?.endpoint ?? config.endpoint;
+
     const { data } = await fetchProject(
-      config.endpoint,
+      endpoint,
       config.apiKey,
-      localProject.uuid ?? localProject.id,
+      trackedProject.uuid!,
       logger
     );
 
     remoteProject = await Project.from('state', data!, {
-      endpoint: config.endpoint,
+      endpoint: endpoint,
     });
 
-    logger.success('Downloaded latest version of project at ', config.endpoint);
+    logger.success('Downloaded latest version of project at ', endpoint);
   } catch (e) {
     console.log(e);
     throw e;
@@ -150,17 +163,6 @@ const syncProjects = async (
     // this will actually happen later
   }
 
-  // warn if the remote UUID is different to the local UUID
-  // This shouldn't happen?
-  if (!options.force && localProject.uuid !== remoteProject.uuid) {
-    logger.error(`UUID conflict!
-
-Your local project (${localProject.uuid}) has a different UUID to the remote project (${remoteProject.uuid}).
-
-Pass --force to override this error and deploy anyway.`);
-    process.exit(1);
-  }
-
   const locallyChangedWorkflows = await findLocallyChangedWorkflows(
     ws,
     localProject
@@ -183,9 +185,9 @@ Pass --force to override this error and deploy anyway.`);
   // Skip divergence testing if the remote has no history in its workflows
   // (this will only happen on older versions of lightning)
   // TODO now maybe skip if there's no forked_from
-  const skipVersionTest = remoteProject.workflows.find(
-    (wf) => wf.history.length === 0
-  );
+  const skipVersionTest =
+    options.force ||
+    remoteProject.workflows.find((wf) => wf.history.length === 0);
 
   if (skipVersionTest) {
     logger.warn(
@@ -222,10 +224,11 @@ Pass --force to override this error and deploy anyway.`);
   }
 
   logger.info('Merging changes into remote project');
-
   // TODO I would like to log which workflows are being updated
   const merged = Project.merge(localProject, remoteProject!, {
-    mode: 'replace',
+    // If pushing the same project, we use a replace strategy
+    // Otherwise, use the sandbox strategy to preserve UUIDs
+    mode: localProject.uuid === remoteProject.uuid ? 'replace' : 'sandbox',
     force: true,
     onlyUpdated: true,
   });
@@ -252,7 +255,34 @@ export async function handler(options: DeployOptions, logger: Logger) {
     name: options.name,
   });
 
+  // Track the remote we want to target
+  // If the used passed a project alias, we need to use that
+  // Otherwise just sync with the local project
+  const tracker = ws.get(options.project ?? localProject.uuid!);
+
+  if (!tracker) {
+    // Is this really an error? Unlikely to happen I thuink
+    console.log(
+      `ERROR: Failed to find tracked remote project ${
+        options.project ?? localProject.uuid!
+      } locally`
+    );
+    console.log('To deploy a new project, add --new to the command');
+    // TODO can we automate the fetch bit?
+    // If it's a UUID it should be ok?
+    console.log(
+      'You may need to fetch the project before you can safely deploy'
+    );
+
+    throw new Error('Failed to find remote project locally');
+  }
+
+  let endpoint: string = tracker.openfn?.endpoint ?? '';
+
   if (options.new) {
+    endpoint =
+      config.endpoint ?? localProject.openfn?.endpoint ?? DEFAULT_ENDPOINT;
+
     // reset all metadata
     localProject.openfn = {
       endpoint: config.endpoint,
@@ -261,11 +291,13 @@ export async function handler(options: DeployOptions, logger: Logger) {
   // generate a credential map
   localProject.credentials = localProject.buildCredentialMap();
 
-  logger.success(`Loaded local project ${printProjectName(localProject)}`);
+  logger.success(
+    `Loaded checked-out project ${printProjectName(localProject)}`
+  );
 
   const merged: Project = options.new
     ? localProject
-    : await syncProjects(options, config, ws, localProject, logger);
+    : await syncProjects(options, config, ws, localProject, tracker, logger);
 
   const state = merged.serialize('state', {
     format: 'json',
@@ -279,9 +311,6 @@ export async function handler(options: DeployOptions, logger: Logger) {
   logger.debug(JSON.stringify(state, null, 2));
   logger.debug();
 
-  // TODO not totally sold on endpoint handling right now
-  config.endpoint ??= localProject.openfn?.endpoint!;
-
   // TODO: I want to report diff HERE, after the merged state and stuff has been built
 
   if (options.dryRun) {
@@ -292,11 +321,7 @@ export async function handler(options: DeployOptions, logger: Logger) {
     // The following workflows will be updated
 
     if (options.confirm) {
-      if (
-        !(await logger.confirm(
-          `Ready to deploy changes to ${config.endpoint}?`
-        ))
-      ) {
+      if (!(await logger.confirm(`Ready to deploy changes to ${endpoint}?`))) {
         logger.always('Cancelled deployment');
         return false;
       }
@@ -305,7 +330,7 @@ export async function handler(options: DeployOptions, logger: Logger) {
     logger.info('Sending project to app...');
 
     const { data: result } = await deployProject(
-      config.endpoint,
+      endpoint,
       config.apiKey,
       state,
       logger
@@ -315,7 +340,7 @@ export async function handler(options: DeployOptions, logger: Logger) {
       'state',
       result,
       {
-        endpoint: config.endpoint,
+        endpoint: endpoint,
         alias,
       },
       merged.config
@@ -332,7 +357,7 @@ export async function handler(options: DeployOptions, logger: Logger) {
     const fullFinalPath = await serialize(finalProject, finalOutputPath);
     logger.debug('Updated local project at ', fullFinalPath);
 
-    logger.success('Updated project  at', config.endpoint);
+    logger.success('Updated project  at', endpoint);
   }
 }
 
@@ -381,4 +406,3 @@ export const reportDiff = (
 
   return diffs;
 };
-``;
diff --git a/packages/cli/src/projects/merge.ts b/packages/cli/src/projects/merge.ts
index af237a646..6b471e39a 100644
--- a/packages/cli/src/projects/merge.ts
+++ b/packages/cli/src/projects/merge.ts
@@ -50,7 +50,7 @@ const options = [
 const command: yargs.CommandModule = {
   command: 'merge <project>',
   describe:
-    'Merges the specified project (by UUID, id or alias) into the currently checked out project',
+    'Merges the currently checked-out project into the target project, and checks out the result. Does not update the remote project or local project.yaml file',
   handler: ensure('project-merge', options),
   builder: (yargs) => build(options, yargs),
 };
@@ -141,8 +141,6 @@ export const handler = async (options: MergeOptions, logger: Logger) => {
 
   logger.info('Checking out merged project to filesystem');
 
-  // TODO support --no-checkout to merge without expanding
-
   // Checkout after merge to expand updated files into filesystem
   await checkout(
     {
diff --git a/packages/cli/src/projects/util.ts b/packages/cli/src/projects/util.ts
index 47061656b..d325ec7ec 100644
--- a/packages/cli/src/projects/util.ts
+++ b/packages/cli/src/projects/util.ts
@@ -9,6 +9,7 @@ import { CLIError } from '../errors';
 import resolvePath from '../util/resolve-path';
 import { rimraf } from 'rimraf';
 import { versionsEqual, Workspace } from '@openfn/project';
+import { DEFAULT_ENDPOINT } from './deploy';
 
 export type AuthOptions = Pick<Opts, 'apiKey' | 'endpoint'>;
 
@@ -20,7 +21,7 @@ export const loadAppAuthConfig = (
 
   const config: AuthOptions = {
     apiKey: options.apiKey,
-    endpoint: options.endpoint ?? 'https://app.openfn.org',
+    endpoint: options.endpoint ?? DEFAULT_ENDPOINT,
   };
 
   if (!options.apiKey && OPENFN_API_KEY) {
diff --git a/packages/project/CHANGELOG.md b/packages/project/CHANGELOG.md
index 009374793..60ddd603a 100644
--- a/packages/project/CHANGELOG.md
+++ b/packages/project/CHANGELOG.md
@@ -1,5 +1,11 @@
 # @openfn/project
 
+## 0.14.1
+
+### Patch Changes
+
+- 58a9919: Fix an issue where added and removed workflows are ignored by merge
+
 ## 0.14.0
 
 ### Minor Changes
diff --git a/packages/project/package.json b/packages/project/package.json
index 46110dd89..473fbffb3 100644
--- a/packages/project/package.json
+++ b/packages/project/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@openfn/project",
-  "version": "0.14.0",
+  "version": "0.14.1",
   "description": "Read, serialize, replicate and sync OpenFn projects",
   "scripts": {
     "test": "pnpm ava",
diff --git a/packages/project/src/util/find-changed-workflows.ts b/packages/project/src/util/find-changed-workflows.ts
index baa61b2f2..ca22e5ccf 100644
--- a/packages/project/src/util/find-changed-workflows.ts
+++ b/packages/project/src/util/find-changed-workflows.ts
@@ -1,8 +1,9 @@
 import Project from '../Project';
+import type Workflow from '../Workflow';
 import { generateHash } from './version';
 
 /**
- * For a give Project, identify which workflows have changed
+ * For a given Project, identify which workflows have changed
  * Uses forked_from as the base, or history if that's unavailable
  */
 export default (project: Project) => {
@@ -23,8 +24,19 @@ export default (project: Project) => {
       if (hash !== base[wf.id]) {
         changed.push(wf);
       }
+      delete base[wf.id];
+    } else {
+      // If a workflow doens't appear in forked_from, we assume it's new
+      // (and so changed!)
+      changed.push(wf);
     }
   }
 
+  // Anything in forked_from that hasn't been handled
+  // must have been removed (and so changed!)
+  for (const removedId in base) {
+    changed.push({ id: removedId, $deleted: true } as unknown as Workflow);
+  }
+
   return changed;
 };
diff --git a/packages/project/test/merge/merge-project.test.ts b/packages/project/test/merge/merge-project.test.ts
index 1ed4af421..e495f7e32 100644
--- a/packages/project/test/merge/merge-project.test.ts
+++ b/packages/project/test/merge/merge-project.test.ts
@@ -432,6 +432,86 @@ test('should merge two projects and preserve edge id', (t) => {
   t.is(target.getUUID('a-b'), resultEdge.openfn.uuid);
 });
 
+test('merge a new workflow', (t) => {
+  const wf1 = assignUUIDs({
+    name: 'wf1',
+    steps: [],
+  });
+  // Wf2 has no UUIDs
+  const wf2 = {
+    name: 'wf2',
+    steps: [],
+  };
+
+  const main = createProject([wf1], 'a');
+  const staging = createProject([wf1, wf2], 'b');
+  t.is(main.workflows.length, 1)
+  t.is(staging.workflows.length, 2)
+
+  const result = merge(staging, main);
+  t.is(result.workflows.length, 2)
+});
+
+test('merge a new workflow with onlyUpdated: true', (t) => {
+  const wf1 = assignUUIDs({
+    name: 'wf1',
+    steps: [],
+  });
+  // Wf2 has no UUIDs
+  const wf2 = {
+    name: 'wf2',
+    steps: [],
+  };
+
+  const main = createProject([wf1], 'a');
+  const staging = createProject([wf1, wf2], 'b');
+  t.is(main.workflows.length, 1)
+  t.is(staging.workflows.length, 2)
+
+  const result = merge(staging, main, { onlyUpdated: true });
+  t.is(result.workflows.length, 2)
+});
+
+test('remove a workflow', (t) => {
+  const wf1 = assignUUIDs({
+    name: 'wf1',
+    steps: [],
+  });
+  const wf2 = assignUUIDs({
+    name: 'wf2',
+    steps: [],
+  });
+
+  const main = createProject([wf1, wf2], 'a');
+  const staging = createProject([wf1], 'b');
+  
+  t.is(main.workflows.length, 2)
+  t.is(staging.workflows.length, 1)
+
+  const result = merge(staging, main);
+  t.is(result.workflows.length, 1)
+});
+
+test('remove a workflow with onlyUpdated: true', (t) => {
+  const wf1 = assignUUIDs({
+    name: 'wf1',
+    steps: [],
+  });
+  const wf2 = assignUUIDs({
+    name: 'wf2',
+    steps: [],
+  });
+
+  const main = createProject([wf1, wf2], 'a');
+  const staging = createProject([wf1], 'b');
+  
+  t.is(main.workflows.length, 2)
+  t.is(staging.workflows.length, 1)
+
+  const result = merge(staging, main, { onlyUpdated: true });
+  t.is(result.workflows.length, 1)
+});
+
 test('id match: same workflow in source and target project', (t) => {
   const source = generateWorkflow('a-b');
   const target = generateWorkflow('a-b');
diff --git a/packages/project/test/util/find-changed-workflows.test.ts b/packages/project/test/util/find-changed-workflows.test.ts
index c3b144ae9..2ccd969cc 100644
--- a/packages/project/test/util/find-changed-workflows.test.ts
+++ b/packages/project/test/util/find-changed-workflows.test.ts
@@ -36,6 +36,37 @@ test('should return 1 changed workflows from forked_from', (t) => {
   t.is(changed[0].id, 'b');
 });
 
+test('should return 1 removed workflow', (t) => {
+  const project = generateProject('proj', ['@id a a-b', '@id b x-y']);
+  const [a, b] = project.workflows;
+
+  project.cli.forked_from = {
+    [a.id]: generateHash(a),
+    [b.id]: generateHash(b),
+  };
+
+  // remove workflow b
+  project.workflows.pop()
+
+  const changed = findChangedWorkflows(project);
+  t.is(changed.length, 1);
+  t.is(changed[0].id, 'b');
+});
+
+test('should return 1 added workflow', (t) => {
+  const project = generateProject('proj', ['@id a a-b', '@id b x-y']);
+  const [a, b] = project.workflows;
+
+  project.cli.forked_from = {
+    [a.id]: generateHash(a),
+    // Do not include b in forked_from - it's new!
+  };
+
+  const changed = findChangedWorkflows(project);
+  t.is(changed.length, 1);
+  t.is(changed[0].id, 'b');
+});
+
 test.todo('changed from history');
 test.todo('multiple changed workflows');
 test.todo('if no base available, assume a change');