diff --git a/src/datasource/catmaid/spatial_skeleton_commands.ts b/src/datasource/catmaid/spatial_skeleton_commands.ts
index c6103c6f0..14dc8d918 100644
--- a/src/datasource/catmaid/spatial_skeleton_commands.ts
+++ b/src/datasource/catmaid/spatial_skeleton_commands.ts
@@ -916,6 +916,13 @@ async function commitAndApplyDeleteNode(
   if (options.invalidateSourceCells) {
     invalidateDeletedNodeSourceCells(resolvedNode.skeletonLayer, deleteContext);
   }
+  const remainingNodes =
+    layer.spatialSkeletonState.getCachedSegmentNodes(
+      resolvedNode.node.segmentId,
+    ) ?? [];
+  if (remainingNodes.length === 0) {
+    resolvedNode.skeletonLayer.markSegmentEdited(resolvedNode.node.segmentId);
+  }
   return { resolvedNode };
 }
 
@@ -1853,6 +1860,8 @@ class SplitCommand implements SpatialSkeletonCommand {
       [existingSkeletonId, newSkeletonId],
       collectUniqueNodePositions(getSplitAffectedNodes(resolvedNode)),
     );
+    resolvedNode.skeletonLayer.retainOverlaySegment(existingSkeletonId);
+    resolvedNode.skeletonLayer.retainOverlaySegment(newSkeletonId);
     StatusMessage.showTemporaryMessage(
       `${statusPrefix} skeleton ${existingSkeletonId}. New skeleton: ${newSkeletonId}.`,
     );
@@ -1914,7 +1923,7 @@ class SplitCommand implements SpatialSkeletonCommand {
       this.layer.displayState.segmentStatedColors.value.delete(
         BigInt(deletedSkeletonId),
       );
-      splitNode.skeletonLayer.suppressBrowseSegment(deletedSkeletonId);
+      splitNode.skeletonLayer.markSegmentEdited(deletedSkeletonId);
     }
     this.layer.selectSpatialSkeletonNode(
       splitNode.node.nodeId,
@@ -1932,6 +1941,7 @@ class SplitCommand implements SpatialSkeletonCommand {
         formerParent,
       ),
     );
+    splitNode.skeletonLayer.retainOverlaySegment(resultSkeletonId);
     StatusMessage.showTemporaryMessage(
       `${statusPrefix} split at node ${splitNode.node.nodeId}.`,
     );
@@ -2118,7 +2128,7 @@ class MergeCommand implements SpatialSkeletonCommand {
       BigInt(deletedSkeletonId),
     );
     if (deletedSkeletonId !== resultSkeletonId) {
-      firstNode.skeletonLayer.suppressBrowseSegment(deletedSkeletonId);
+      firstNode.skeletonLayer.markSegmentEdited(deletedSkeletonId);
     }
     this.layer.clearSpatialSkeletonMergeAnchor();
     await refreshTopologySegments(
@@ -2126,6 +2136,7 @@ class MergeCommand implements SpatialSkeletonCommand {
       [resultSkeletonId, deletedSkeletonId],
       getMergeAffectedPositions(result.deletedSegmentId, firstNode, secondNode),
     );
+    firstNode.skeletonLayer.retainOverlaySegment(resultSkeletonId);
     const swapSuffix = result.directionAdjusted
       ? " Merge direction was adjusted by the active source."
       : "";
@@ -2223,6 +2234,8 @@ class MergeCommand implements SpatialSkeletonCommand {
           `Only the split completed. ${formatErrorMessage(error)}`;
       }
     }
+    attachedNode.skeletonLayer.retainOverlaySegment(survivingSegmentId);
+    attachedNode.skeletonLayer.retainOverlaySegment(restoredSegmentId);
     this.layer.selectSpatialSkeletonNode(
       attachedNode.node.nodeId,
       this.layer.manager.root.selectionState.pin.value,
diff --git a/src/layer/segmentation/spatial_skeleton_commands.spec.ts b/src/layer/segmentation/spatial_skeleton_commands.spec.ts
index 2e0724b8e..3a4cfe69d 100644
--- a/src/layer/segmentation/spatial_skeleton_commands.spec.ts
+++ b/src/layer/segmentation/spatial_skeleton_commands.spec.ts
@@ -1247,7 +1247,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: makeDisplayState([originalSegmentId]),
@@ -1386,7 +1387,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: {
@@ -1437,7 +1439,7 @@ describe("spatial_skeleton_commands", () => {
       segmentId: originalSegmentId,
     });
 
-    skeletonLayer.suppressBrowseSegment.mockClear();
+    skeletonLayer.markSegmentEdited.mockClear();
     deleteSegmentColor.mockClear();
     layer.selectSpatialSkeletonNode.mockClear();
     layer.markSpatialSkeletonNodeDataChanged.mockClear();
@@ -1458,7 +1460,7 @@ describe("spatial_skeleton_commands", () => {
       }),
     );
     expect(deleteSegmentColor).toHaveBeenCalledWith(BigInt(splitSegmentId));
-    expect(skeletonLayer.suppressBrowseSegment).toHaveBeenCalledWith(
+    expect(skeletonLayer.markSegmentEdited).toHaveBeenCalledWith(
       splitSegmentId,
     );
     expect(layer.selectSpatialSkeletonNode).toHaveBeenCalledWith(
@@ -1607,7 +1609,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: {
@@ -1860,7 +1863,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: {
@@ -2150,7 +2154,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: {
@@ -2349,7 +2354,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: {
@@ -2509,7 +2515,8 @@ describe("spatial_skeleton_commands", () => {
       source: skeletonSource,
       getNode: vi.fn((nodeId: number) => cacheByNode.get(nodeId)),
       invalidateSourceCellsForPositions: vi.fn(),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
     };
     const layer = {
       displayState: makeDisplayState([firstSegmentId, secondSegmentId]),
@@ -2603,7 +2610,8 @@ describe("spatial_skeleton_commands", () => {
         if (nodeId === secondNode.nodeId) return secondNode;
         return undefined;
       }),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
       invalidateSourceCellsForPositions: vi.fn(),
     };
     const layer = {
diff --git a/src/skeleton/frontend.spec.ts b/src/skeleton/frontend.spec.ts
index d6670a78d..7b9aa56b3 100644
--- a/src/skeleton/frontend.spec.ts
+++ b/src/skeleton/frontend.spec.ts
@@ -299,19 +299,18 @@ describe("SpatiallyIndexedSkeletonLayer targeted source invalidation", () => {
 });
 
 describe("SpatiallyIndexedSkeletonLayer browse exclusions", () => {
-  it("includes suppressed browse segments even when no overlay segment is loaded", () => {
+  it("includes edited segments in browse exclusions regardless of cache state", () => {
     const layer = Object.assign(
       Object.create(SpatiallyIndexedSkeletonLayer.prototype),
       {
-        suppressedBrowseSegmentIds: new Set<number>(),
+        editedSegmentIds: new Set<number>(),
         browseExcludedSegments: new Uint64Set(),
         browseExcludedSegmentsKey: undefined,
         redrawNeeded: { dispatch: vi.fn() },
-        getLoadedOverlaySegmentIds: () => [],
       },
     );
 
-    expect(layer.suppressBrowseSegment(29)).toBe(true);
+    expect(layer.markSegmentEdited(29)).toBe(true);
     expect(layer.redrawNeeded.dispatch).toHaveBeenCalledTimes(1);
 
     const excludedSegments = (layer as any).getBrowsePassExcludedSegments();
diff --git a/src/skeleton/frontend.ts b/src/skeleton/frontend.ts
index 6d850f128..177ae1205 100644
--- a/src/skeleton/frontend.ts
+++ b/src/skeleton/frontend.ts
@@ -2071,7 +2071,7 @@ export class SpatiallyIndexedSkeletonLayer
   private browseExcludedSegments = new Uint64Set();
   private gpuBrowseExcludedSegmentsHashTable: GPUHashTable<HashSetUint64>;
   private browseExcludedSegmentsKey: string | undefined;
-  private suppressedBrowseSegmentIds = new Set<number>();
+  private readonly editedSegmentIds = new Set<number>();
   private retainedOverlaySegmentIds: number[] = [];
   private maxRetainedOverlaySegments: number;
   private readonly selectedNodeOutlineColor = vec3.clone(
@@ -2159,6 +2159,7 @@ export class SpatiallyIndexedSkeletonLayer
   }
 
   retainOverlaySegment(segmentId: number) {
+    this.markSegmentEdited(segmentId);
     const nextRetainedOverlaySegmentIds =
       retainSpatiallyIndexedSkeletonOverlaySegment(
         this.retainedOverlaySegmentIds,
@@ -2180,16 +2181,16 @@ export class SpatiallyIndexedSkeletonLayer
     return true;
   }
 
-  suppressBrowseSegment(segmentId: number) {
+  markSegmentEdited(segmentId: number) {
     const normalizedSegmentId = Math.round(Number(segmentId));
     if (
       !Number.isSafeInteger(normalizedSegmentId) ||
       normalizedSegmentId <= 0 ||
-      this.suppressedBrowseSegmentIds.has(normalizedSegmentId)
+      this.editedSegmentIds.has(normalizedSegmentId)
     ) {
       return false;
     }
-    this.suppressedBrowseSegmentIds.add(normalizedSegmentId);
+    this.editedSegmentIds.add(normalizedSegmentId);
     this.redrawNeeded.dispatch();
     return true;
   }
@@ -2201,41 +2202,8 @@ export class SpatiallyIndexedSkeletonLayer
     );
   }
 
-  private getLoadedOverlaySegmentIds(
-    segmentIds: readonly number[] = this.getOverlayRenderSegmentIds(),
-  ) {
-    if (this.inspectionState === undefined) {
-      return [];
-    }
-    return segmentIds.filter(
-      (segmentId) =>
-        this.inspectionState?.getCachedSegmentNodes(segmentId) !== undefined,
-    );
-  }
-
   private getNormalizedBrowsePassExcludedSegmentIds() {
-    const segmentIds = new Set<number>();
-    for (const segmentId of this.getLoadedOverlaySegmentIds()) {
-      const normalizedSegmentId = Math.round(Number(segmentId));
-      if (
-        !Number.isSafeInteger(normalizedSegmentId) ||
-        normalizedSegmentId <= 0
-      ) {
-        continue;
-      }
-      segmentIds.add(normalizedSegmentId);
-    }
-    for (const segmentId of this.suppressedBrowseSegmentIds) {
-      const normalizedSegmentId = Math.round(Number(segmentId));
-      if (
-        !Number.isSafeInteger(normalizedSegmentId) ||
-        normalizedSegmentId <= 0
-      ) {
-        continue;
-      }
-      segmentIds.add(normalizedSegmentId);
-    }
-    return [...segmentIds].sort((a, b) => a - b);
+    return [...this.editedSegmentIds].sort((a, b) => a - b);
   }
 
   private getBrowsePassExcludedSegments() {
diff --git a/src/ui/skeleton_edit_tools.spec.ts b/src/ui/skeleton_edit_tools.spec.ts
index a1e6b6c19..d84ce9941 100644
--- a/src/ui/skeleton_edit_tools.spec.ts
+++ b/src/ui/skeleton_edit_tools.spec.ts
@@ -564,7 +564,8 @@ describe("spatial_skeleton_edit_tool", () => {
         if (nodeId === secondNode.nodeId) return secondNode;
         return undefined;
       }),
-      suppressBrowseSegment: vi.fn(),
+      markSegmentEdited: vi.fn(),
+      retainOverlaySegment: vi.fn(),
       invalidateSourceCellsForPositions: vi.fn(),
     };
     const commandHistory = new SpatialSkeletonCommandHistory();
@@ -634,7 +635,7 @@ describe("spatial_skeleton_edit_tool", () => {
       segmentId: 17,
     });
     expect(deleteSegmentColor).toHaveBeenCalledWith(11n);
-    expect(skeletonLayer.suppressBrowseSegment).toHaveBeenCalledWith(11);
+    expect(skeletonLayer.markSegmentEdited).toHaveBeenCalledWith(11);
     expect(markSpatialSkeletonNodeDataChanged).toHaveBeenCalledWith({
       invalidateFullSkeletonCache: false,
     });
diff --git a/src/ui/skeleton_edit_tools.ts b/src/ui/skeleton_edit_tools.ts
index fe5e88f5f..234bc6189 100644
--- a/src/ui/skeleton_edit_tools.ts
+++ b/src/ui/skeleton_edit_tools.ts
@@ -1024,6 +1024,7 @@ export class SpatialSkeletonEditModeTool extends SpatialSkeletonToolBase {
               )
                 return;
               dragStarted = true;
+              skeletonLayer.markSegmentEdited(nodeInfo.segmentId);
             }
             dragPanel.translateDataPointByViewportPixels(
               this.dragGlobalPosition,