diff --git a/frontend/src/components/shared/rightRail/ViewerAnnotationControls.tsx b/frontend/src/components/shared/rightRail/ViewerAnnotationControls.tsx
index 42dbbb5a8..0b9d9a754 100644
--- a/frontend/src/components/shared/rightRail/ViewerAnnotationControls.tsx
+++ b/frontend/src/components/shared/rightRail/ViewerAnnotationControls.tsx
@@ -10,6 +10,7 @@ import { useFileState, useFileContext } from '../../../contexts/FileContext';
 import { generateThumbnailWithMetadata } from '../../../utils/thumbnailUtils';
 import { createProcessedFile } from '../../../contexts/file/fileActions';
 import { createStirlingFile, createNewStirlingFileStub } from '../../../types/fileContext';
+import { useNavigationState } from '../../../contexts/NavigationContext';
 
 interface ViewerAnnotationControlsProps {
   currentView: string;
@@ -32,6 +33,10 @@ export default function ViewerAnnotationControls({ currentView }: ViewerAnnotati
   const { actions: fileActions } = useFileContext();
   const activeFiles = selectors.getFiles();
 
+  // Check if we're in sign mode
+  const { selectedTool } = useNavigationState();
+  const isSignMode = selectedTool === 'sign';
+
   // Turn off annotation mode when switching away from viewer
   useEffect(() => {
     if (currentView !== 'viewer' && viewerContext?.isAnnotationMode) {
@@ -39,6 +44,11 @@ export default function ViewerAnnotationControls({ currentView }: ViewerAnnotati
     }
   }, [currentView, viewerContext]);
 
+  // Don't show any annotation controls in sign mode
+  if (isSignMode) {
+    return null;
+  }
+
   return (
     <>
       {/* Annotation Visibility Toggle */}
diff --git a/frontend/src/components/tools/sign/SignSettings.tsx b/frontend/src/components/tools/sign/SignSettings.tsx
index 9585bad1c..1bc72d840 100644
--- a/frontend/src/components/tools/sign/SignSettings.tsx
+++ b/frontend/src/components/tools/sign/SignSettings.tsx
@@ -116,6 +116,13 @@ const SignSettings = ({
     }
   }, [parameters.signatureType, parameters.signerName, parameters.fontSize, parameters.fontFamily, onActivateSignaturePlacement, onDeactivateSignature]);
 
+  // Reset to move mode when placement mode is deactivated
+  useEffect(() => {
+    if (!isPlacementMode && interactionMode === 'place') {
+      setInteractionMode('move');
+    }
+  }, [isPlacementMode, interactionMode]);
+
   // Handle signature data updates
   useEffect(() => {
     let newSignatureData: string | undefined = undefined;
@@ -288,7 +295,10 @@ const SignSettings = ({
       {/* Apply Signatures Button */}
       {onSave && (
         <Button
-          onClick={onSave}
+          onClick={() => {
+            console.log('Apply Signatures button clicked');
+            onSave();
+          }}
           color="blue"
           variant="filled"
           fullWidth
diff --git a/frontend/src/contexts/file/FileReducer.ts b/frontend/src/contexts/file/FileReducer.ts
index 0818df704..97a2c753d 100644
--- a/frontend/src/contexts/file/FileReducer.ts
+++ b/frontend/src/contexts/file/FileReducer.ts
@@ -51,8 +51,9 @@ function processFileSwap(
     }
   });
 
-  // Clear selections that reference removed files
+  // Clear selections that reference removed files and add new files to selection
   const validSelectedFileIds = state.ui.selectedFileIds.filter(id => !unpinnedRemoveIds.includes(id));
+  const newSelectedFileIds = [...validSelectedFileIds, ...addedIds];
 
   return {
     ...state,
@@ -62,7 +63,7 @@ function processFileSwap(
     },
     ui: {
       ...state.ui,
-      selectedFileIds: validSelectedFileIds
+      selectedFileIds: newSelectedFileIds
     }
   };
 }
diff --git a/frontend/src/tools/Sign.tsx b/frontend/src/tools/Sign.tsx
index 87f784d6f..5b68f9f38 100644
--- a/frontend/src/tools/Sign.tsx
+++ b/frontend/src/tools/Sign.tsx
@@ -15,9 +15,10 @@ import { flattenSignatures } from "../utils/signatureFlattening";
 const Sign = (props: BaseToolProps) => {
   const { t } = useTranslation();
   const { setWorkbench } = useNavigation();
-  const { setSignatureConfig, activateDrawMode, activateSignaturePlacementMode, deactivateDrawMode, updateDrawSettings, undo, redo, signatureApiRef, getImageData, setSignaturesApplied } = useSignature();
+  const { setSignatureConfig, activateDrawMode, activateSignaturePlacementMode, deactivateDrawMode, updateDrawSettings, undo, redo, signatureApiRef, getImageData, setSignaturesApplied, historyApiRef } = useSignature();
   const { consumeFiles, selectors } = useFileContext();
   const { exportActions, getScrollState } = useViewer();
+  const { setHasUnsavedChanges, unregisterUnsavedChangesChecker } = useNavigation();
 
   // Track which signature mode was active for reactivation after save
   const activeModeRef = useRef<'draw' | 'placement' | null>(null);
@@ -38,6 +39,11 @@ const Sign = (props: BaseToolProps) => {
     handleSignaturePlacement();
   }, [handleSignaturePlacement]);
 
+  const handleDeactivateSignature = useCallback(() => {
+    activeModeRef.current = null;
+    deactivateDrawMode();
+  }, [deactivateDrawMode]);
+
   const base = useBaseTool(
     'sign',
     useSignParameters,
@@ -65,6 +71,17 @@ const Sign = (props: BaseToolProps) => {
   // Save signed files to the system - apply signatures using EmbedPDF and replace original
   const handleSaveToSystem = useCallback(async () => {
     try {
+      console.log('=== Apply Signatures Started ===');
+      console.log('exportActions:', exportActions);
+      console.log('signatureApiRef.current:', signatureApiRef.current);
+
+      // Deactivate signature placement mode immediately
+      handleDeactivateSignature();
+
+      // Unregister unsaved changes checker to prevent warning during apply
+      unregisterUnsavedChangesChecker();
+      setHasUnsavedChanges(false);
+
       // Get the original file
       let originalFile = null;
       if (base.selectedFiles.length > 0) {
@@ -84,8 +101,10 @@ const Sign = (props: BaseToolProps) => {
         return;
       }
 
+      console.log('originalFile:', originalFile);
+
       // Use the signature flattening utility
-      const success = await flattenSignatures({
+      const newFileIds = await flattenSignatures({
         signatureApiRef,
         getImageData,
         exportActions,
@@ -95,34 +114,26 @@ const Sign = (props: BaseToolProps) => {
         getScrollState
       });
 
-      if (success) {
+      console.log('flattenSignatures result:', newFileIds);
+
+      if (newFileIds && newFileIds.length > 0) {
         console.log('✓ Signature flattening completed successfully');
 
         // Mark signatures as applied
         setSignaturesApplied(true);
 
-        // Force refresh the viewer to show the flattened PDF
+        // Force viewer reload to show flattened PDF
+        setWorkbench('fileEditor');
         setTimeout(() => {
-          // Navigate away from viewer and back to force reload
-          setWorkbench('fileEditor');
-          setTimeout(() => {
-            setWorkbench('viewer');
-
-            // Reactivate the signature mode that was active before save
-            if (activeModeRef.current === 'draw') {
-              activateDrawMode();
-            } else if (activeModeRef.current === 'placement') {
-              handleSignaturePlacement();
-            }
-          }, 100);
-        }, 200);
+          setWorkbench('viewer');
+        }, 50);
       } else {
         console.error('Signature flattening failed');
       }
     } catch (error) {
       console.error('Error saving signed document:', error);
     }
-  }, [exportActions, base.selectedFiles, selectors, consumeFiles, signatureApiRef, getImageData, setWorkbench, activateDrawMode]);
+  }, [exportActions, base.selectedFiles, selectors, consumeFiles, signatureApiRef, getImageData, setWorkbench, activateDrawMode, setSignaturesApplied, getScrollState, handleDeactivateSignature, setHasUnsavedChanges, unregisterUnsavedChangesChecker]);
 
   const getSteps = () => {
     const steps = [];
@@ -140,7 +151,7 @@ const Sign = (props: BaseToolProps) => {
             disabled={base.endpointLoading}
             onActivateDrawMode={handleActivateDrawMode}
             onActivateSignaturePlacement={handleActivateSignaturePlacement}
-            onDeactivateSignature={deactivateDrawMode}
+            onDeactivateSignature={handleDeactivateSignature}
             onUpdateDrawSettings={updateDrawSettings}
             onUndo={undo}
             onRedo={redo}
diff --git a/frontend/src/utils/signatureFlattening.ts b/frontend/src/utils/signatureFlattening.ts
index fd7e701a6..85b41f769 100644
--- a/frontend/src/utils/signatureFlattening.ts
+++ b/frontend/src/utils/signatureFlattening.ts
@@ -1,6 +1,6 @@
 import { PDFDocument, rgb } from 'pdf-lib';
 import { generateThumbnailWithMetadata } from './thumbnailUtils';
-import { createProcessedFile } from '../contexts/file/fileActions';
+import { createProcessedFile, createChildStub } from '../contexts/file/fileActions';
 import { createNewStirlingFileStub, createStirlingFile, StirlingFile, FileId, StirlingFileStub } from '../types/fileContext';
 import type { SignatureAPI } from '../components/viewer/SignatureAPIBridge';
 
@@ -22,7 +22,7 @@ interface SignatureFlatteningOptions {
   getScrollState: () => { currentPage: number; totalPages: number };
 }
 
-export async function flattenSignatures(options: SignatureFlatteningOptions): Promise<boolean> {
+export async function flattenSignatures(options: SignatureFlatteningOptions): Promise<FileId[] | null> {
   const { signatureApiRef, getImageData, exportActions, selectors, consumeFiles, originalFile, getScrollState } = options;
 
   try {
@@ -85,7 +85,7 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
     // Step 3: Use EmbedPDF's saveAsCopy to get the base PDF (now without annotations)
     if (!exportActions) {
       console.error('No export actions available');
-      return false;
+      return null;
     }
     const pdfArrayBuffer = await exportActions.saveAsCopy();
 
@@ -111,7 +111,7 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
 
       if (!currentFile) {
         console.error('No file available to replace');
-        return false;
+        return null;
       }
 
       let signedFile = new File([blob], currentFile.name, { type: 'application/pdf' });
@@ -150,9 +150,11 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
 
           const pages = pdfDoc.getPages();
 
+          console.log('Starting to render annotations. Total pages with annotations:', allAnnotations.length);
 
           for (const pageData of allAnnotations) {
             const { pageIndex, annotations } = pageData;
+            console.log(`Rendering ${annotations.length} annotations on page ${pageIndex}`);
 
             if (pageIndex < pages.length) {
               const page = pages[pageIndex];
@@ -187,8 +189,18 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
                       }
                     }
 
+                    console.log('Processing annotation:', {
+                      pageIndex,
+                      hasImageData: !!imageDataUrl,
+                      imageDataType: typeof imageDataUrl,
+                      startsWithDataImage: imageDataUrl && typeof imageDataUrl === 'string' && imageDataUrl.startsWith('data:image'),
+                      position: { pdfX, pdfY, width, height }
+                    });
+
                     if (imageDataUrl && typeof imageDataUrl === 'string' && imageDataUrl.startsWith('data:image')) {
                       try {
+                        console.log('Rendering image annotation at:', { pdfX, pdfY, width, height });
+
                         // Convert data URL to bytes
                         const base64Data = imageDataUrl.split(',')[1];
                         const imageBytes = Uint8Array.from(atob(base64Data), c => c.charCodeAt(0));
@@ -211,10 +223,13 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
                           height: height,
                         });
 
+                        console.log('✓ Successfully rendered image annotation');
+
                       } catch (imageError) {
                         console.error('Failed to render image annotation:', imageError);
                       }
                     } else if (annotation.content || annotation.text) {
+                      console.warn('Rendering text annotation instead');
                       // Handle text annotations
                       page.drawText(annotation.content || annotation.text, {
                         x: pdfX,
@@ -287,23 +302,35 @@ export async function flattenSignatures(options: SignatureFlatteningOptions): Pr
       const record = selectors.getStirlingFileStub(currentFile.fileId);
       if (!record) {
         console.error('No file record found for:', currentFile.fileId);
-        return false;
+        return null;
       }
 
-      // Create output stub and file
-      const outputStub = createNewStirlingFileStub(signedFile, undefined, thumbnailResult.thumbnail, processedFileMetadata);
+      console.log('Parent file record:', record);
+      console.log('Parent version:', record.versionNumber);
+
+      // Create output stub and file as a child of the original (increments version)
+      const outputStub = createChildStub(
+        record,
+        { toolId: 'sign', timestamp: Date.now() },
+        signedFile,
+        thumbnailResult.thumbnail,
+        processedFileMetadata
+      );
       const outputStirlingFile = createStirlingFile(signedFile, outputStub.id);
 
-      // Replace the original file with the signed version
-      await consumeFiles(inputFileIds, [outputStirlingFile], [outputStub]);
+      console.log('Output stub version:', outputStub.versionNumber);
+      console.log('Consuming files - replacing:', inputFileIds, 'with:', outputStub.id);
 
-      console.log('✓ Signature flattening completed successfully');
-      return true;
+      // Replace the original file with the signed version
+      const newFileIds = await consumeFiles(inputFileIds, [outputStirlingFile], [outputStub]);
+
+      console.log('✓ Signature flattening completed successfully. New file IDs:', newFileIds);
+      return newFileIds;
     }
 
-    return false;
+    return null;
   } catch (error) {
     console.error('Error flattening signatures:', error);
-    return false;
+    return null;
   }
 }
\ No newline at end of file