diff --git a/pkg/datastore/sync.go b/pkg/datastore/sync.go
index c252b1bc..6017a9db 100644
--- a/pkg/datastore/sync.go
+++ b/pkg/datastore/sync.go
@@ -2,6 +2,7 @@ package datastore
 
 import (
 	"context"
+	"errors"
 	"sync"
 
 	"github.com/sdcio/data-server/pkg/tree"
@@ -29,7 +30,11 @@ func (d *Datastore) ApplyToRunning(ctx context.Context, deletes []*sdcpb.Path, i
 	for _, delete := range deletes {
 		// navigate to delete path
 		deleteRoot, err := ops.NavigateSdcpbPath(ctx, d.syncTree.Entry, delete)
-		if err != nil {
+		switch {
+		case errors.Is(err, ops.ErrNavigateSdcpbPathNotFound):
+			log.V(logger.VDebug).Info("skipping delete config subtree from internal running with no content", "path", delete.ToXPath(false))
+			continue
+		case err != nil:
 			log.Error(err, "failed navigating to delete path", "path", delete.ToXPath(false))
 			continue
 		}
diff --git a/pkg/tree/ops/navigatesdcpbpath.go b/pkg/tree/ops/navigatesdcpbpath.go
index 2ae4e6b2..379cf67b 100644
--- a/pkg/tree/ops/navigatesdcpbpath.go
+++ b/pkg/tree/ops/navigatesdcpbpath.go
@@ -10,6 +10,10 @@ import (
 	sdcpb "github.com/sdcio/sdc-protos/sdcpb"
 )
 
+var (
+	ErrNavigateSdcpbPathNotFound = fmt.Errorf("path not found in tree")
+)
+
 func NavigateSdcpbPath(ctx context.Context, e api.Entry, path *sdcpb.Path) (api.Entry, error) {
 	pathElems := path.GetElem()
 	var err error
@@ -40,7 +44,7 @@ func NavigateSdcpbPath(ctx context.Context, e api.Entry, path *sdcpb.Path) (api.
 		child, exists := e.GetChilds(types.DescendMethodActiveChilds)[pathElems[0].Name]
 		if !exists {
 			pth := &sdcpb.Path{Elem: pathElems}
-			return nil, fmt.Errorf("navigating tree, reached %v but child %v does not exist, trying to load defaults yielded %v", e.SdcpbPath().ToXPath(false), pth.ToXPath(false), err)
+			return nil, fmt.Errorf("%w: reached %v but child %v does not exist. Trying to load defaults failed", ErrNavigateSdcpbPathNotFound, e.SdcpbPath().ToXPath(false), pth.ToXPath(false))
 		}
 
 		for v := range pathElems[0].PathElemNamesKeysOnly() {