diff --git a/src/cli/commands/init.ts b/src/cli/commands/init.ts
index ff74e07..96af896 100644
--- a/src/cli/commands/init.ts
+++ b/src/cli/commands/init.ts
@@ -21,7 +21,7 @@ import {
 } from '../utils/post-install.js';
 import { DEVFLOW_PLUGINS, LEGACY_SKILL_NAMES, LEGACY_COMMAND_NAMES, buildAssetMaps, type PluginDefinition } from '../plugins.js';
 import { detectPlatform, detectShell, getProfilePath, getSafeDeleteInfo, hasSafeDelete } from '../utils/safe-delete.js';
-import { generateSafeDeleteBlock, isAlreadyInstalled, installToProfile } from '../utils/safe-delete-install.js';
+import { generateSafeDeleteBlock, isAlreadyInstalled, installToProfile, removeFromProfile, getInstalledVersion, SAFE_DELETE_BLOCK_VERSION } from '../utils/safe-delete-install.js';
 import { addAmbientHook, removeAmbientHook, hasAmbientHook } from './ambient.js';
 import { addMemoryHooks, removeMemoryHooks, hasMemoryHooks } from './memory.js';
 
@@ -507,14 +507,19 @@ export const initCommand = new Command('init')
           p.log.info(`Install ${color.cyan(safeDeleteInfo.command ?? 'trash')} first: ${color.dim(safeDeleteInfo.installHint)}`);
           p.log.info(`Then re-run ${color.cyan('devflow init')} to auto-configure safe-delete.`);
         } else if (safeDeleteAvailable) {
-          const alreadyInstalled = await isAlreadyInstalled(profilePath);
-          if (alreadyInstalled) {
-            p.log.info(`Safe-delete already configured in ${color.dim(profilePath)}`);
-          } else {
-            const trashCmd = safeDeleteInfo.command;
-            const block = generateSafeDeleteBlock(shell, process.platform, trashCmd);
-
-            if (block) {
+          const trashCmd = safeDeleteInfo.command;
+          const block = generateSafeDeleteBlock(shell, process.platform, trashCmd);
+
+          if (block) {
+            const installedVersion = await getInstalledVersion(profilePath);
+            if (installedVersion === SAFE_DELETE_BLOCK_VERSION) {
+              p.log.info(`Safe-delete already configured in ${color.dim(profilePath)}`);
+            } else if (installedVersion > 0) {
+              await removeFromProfile(profilePath);
+              await installToProfile(profilePath, block);
+              p.log.success(`Safe-delete upgraded in ${color.dim(profilePath)}`);
+              p.log.info('Restart your shell or run: ' + color.cyan(`source ${profilePath}`));
+            } else {
               const confirm = await p.confirm({
                 message: `Install safe-delete to ${profilePath}? (overrides rm to use ${trashCmd ?? 'recycle bin'})`,
                 initialValue: true,
diff --git a/src/cli/utils/safe-delete-install.ts b/src/cli/utils/safe-delete-install.ts
index c752ccb..69260c8 100644
--- a/src/cli/utils/safe-delete-install.ts
+++ b/src/cli/utils/safe-delete-install.ts
@@ -5,6 +5,9 @@ import type { Shell } from './safe-delete.js';
 const START_MARKER = '# >>> DevFlow safe-delete >>>';
 const END_MARKER = '# <<< DevFlow safe-delete <<<';
 
+/** Bump this when the safe-delete block changes. */
+export const SAFE_DELETE_BLOCK_VERSION = 2;
+
 /**
  * Generate the safe-delete shell function block with markers.
  * Returns null for unsupported shells.
@@ -20,6 +23,7 @@ export function generateSafeDeleteBlock(
     const cmd = trashCommand ?? 'trash';
     return [
       START_MARKER,
+      `# v${SAFE_DELETE_BLOCK_VERSION}`,
       `rm() {`,
       `  local files=()`,
       `  for arg in "$@"; do`,
@@ -48,6 +52,7 @@ export function generateSafeDeleteBlock(
     const cmd = trashCommand ?? 'trash';
     return [
       START_MARKER,
+      `# v${SAFE_DELETE_BLOCK_VERSION}`,
       `function rm --description "Safe delete via trash"`,
       `  set -l files`,
       `  for arg in $argv`,
@@ -73,6 +78,7 @@ export function generateSafeDeleteBlock(
     if (platform === 'win32') {
       return [
         START_MARKER,
+        `# v${SAFE_DELETE_BLOCK_VERSION}`,
         `if (Get-Alias rm -ErrorAction SilentlyContinue) {`,
         `  Remove-Alias rm -Force -Scope Global`,
         `}`,
@@ -101,6 +107,7 @@ export function generateSafeDeleteBlock(
     const cmd = trashCommand ?? 'trash';
     return [
       START_MARKER,
+      `# v${SAFE_DELETE_BLOCK_VERSION}`,
       `if (Get-Alias rm -ErrorAction SilentlyContinue) {`,
       `  Remove-Alias rm -Force -Scope Global`,
       `}`,
@@ -147,6 +154,23 @@ export async function installToProfile(profilePath: string, block: string): Prom
   await fs.writeFile(profilePath, content, 'utf-8');
 }
 
+/**
+ * Extract the installed safe-delete block version from a profile file.
+ * Returns 0 (not installed), 1 (legacy block without version stamp), or N (versioned block).
+ */
+export async function getInstalledVersion(profilePath: string): Promise<number> {
+  try {
+    const content = await fs.readFile(profilePath, 'utf-8');
+    const startIdx = content.indexOf(START_MARKER);
+    if (startIdx === -1) return 0;
+    const afterMarker = content.slice(startIdx + START_MARKER.length);
+    const match = afterMarker.match(/^\n# v(\d+)/);
+    return match ? parseInt(match[1], 10) : 1;
+  } catch {
+    return 0;
+  }
+}
+
 /**
  * Remove the safe-delete block from a profile file.
  * Returns true if the block was found and removed, false otherwise.
diff --git a/tests/safe-delete-install.test.ts b/tests/safe-delete-install.test.ts
index 38d6c5d..83cf4a8 100644
--- a/tests/safe-delete-install.test.ts
+++ b/tests/safe-delete-install.test.ts
@@ -7,6 +7,8 @@ import {
   isAlreadyInstalled,
   installToProfile,
   removeFromProfile,
+  getInstalledVersion,
+  SAFE_DELETE_BLOCK_VERSION,
 } from '../src/cli/utils/safe-delete-install.js';
 
 describe('generateSafeDeleteBlock', () => {
@@ -64,6 +66,64 @@ describe('generateSafeDeleteBlock', () => {
   it('returns null for unknown shell', () => {
     expect(generateSafeDeleteBlock('unknown', 'darwin', 'trash')).toBeNull();
   });
+
+  it('includes version stamp in all shell variants', () => {
+    const versionLine = `# v${SAFE_DELETE_BLOCK_VERSION}`;
+    const variants: Array<[Parameters<typeof generateSafeDeleteBlock>[0], NodeJS.Platform, string | null]> = [
+      ['bash', 'linux', 'trash-put'],
+      ['zsh', 'darwin', 'trash'],
+      ['fish', 'darwin', 'trash'],
+      ['powershell', 'win32', null],
+      ['powershell', 'darwin', 'trash'],
+    ];
+    for (const [shell, platform, cmd] of variants) {
+      const block = generateSafeDeleteBlock(shell, platform, cmd);
+      expect(block, `${shell}/${platform} should include version stamp`).toContain(versionLine);
+    }
+  });
+});
+
+describe('getInstalledVersion', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await fs.mkdtemp(path.join(os.tmpdir(), 'safe-delete-test-'));
+  });
+
+  afterEach(async () => {
+    await fs.rm(tmpDir, { recursive: true, force: true });
+  });
+
+  it('returns 0 for missing file', async () => {
+    expect(await getInstalledVersion(path.join(tmpDir, 'nonexistent'))).toBe(0);
+  });
+
+  it('returns 0 for file without markers', async () => {
+    const filePath = path.join(tmpDir, '.zshrc');
+    await fs.writeFile(filePath, 'some unrelated content\n');
+    expect(await getInstalledVersion(filePath)).toBe(0);
+  });
+
+  it('returns 1 for legacy block without version line', async () => {
+    const filePath = path.join(tmpDir, '.zshrc');
+    await fs.writeFile(filePath, [
+      '# >>> DevFlow safe-delete >>>',
+      'rm() { trash "$@"; }',
+      '# <<< DevFlow safe-delete <<<',
+    ].join('\n'));
+    expect(await getInstalledVersion(filePath)).toBe(1);
+  });
+
+  it('returns version number for versioned block', async () => {
+    const filePath = path.join(tmpDir, '.zshrc');
+    await fs.writeFile(filePath, [
+      '# >>> DevFlow safe-delete >>>',
+      '# v2',
+      'rm() { trash "$@"; }',
+      '# <<< DevFlow safe-delete <<<',
+    ].join('\n'));
+    expect(await getInstalledVersion(filePath)).toBe(2);
+  });
 });
 
 describe('isAlreadyInstalled', () => {