diff --git a/electron/index.html b/electron/index.html
index 9111a81..ee1ccdb 100644
--- a/electron/index.html
+++ b/electron/index.html
@@ -116,6 +116,15 @@
                 <button class="modal-close" onclick="hideSaveOptionsModal()">&times;</button>
             </div>
             <div class="modal-body">
+                <div id="signature-warning-section" class="signature-warning-section hidden">
+                    <div class="warning-banner">
+                        <span class="warning-icon">⚠️</span>
+                        <div class="warning-text">
+                            <strong>Signature Warning:</strong> This operation will invalidate the bundle's digital signature. 
+                            You will need to re-sign the bundle using the <strong>Sign</strong> button and a <strong>PEM private key</strong> file.
+                        </div>
+                    </div>
+                </div>
                 <p>How would you like to save your metadata changes?</p>
                 <div class="save-options">
                     <button id="overwrite-bundle-btn" class="save-option-btn primary">
@@ -131,18 +140,37 @@
         </div>
     </div>
 
-    <!-- Fill Modal -->
+    <!-- Signature Invalidation Warning Modal -->
+    <div id="signature-warning-modal" class="modal-container hidden">
+        <div class="modal-content">
+            <h2>⚠️ Signature Warning</h2>
+            <div class="warning-content">
+                <p><strong>This operation will invalidate the bundle's digital signature.</strong></p>
+                <p>After making changes, you will need to re-sign the bundle using:</p>
+                <ul>
+                    <li>The <strong>Sign</strong> button in the action bar</li>
+                    <li>A valid <strong>PEM private key</strong> file</li>
+                </ul>
+                <p>Do you want to continue?</p>
+            </div>
+            <div class="modal-actions">
+                <button id="signature-warning-cancel" class="action-button secondary">Cancel</button>
+                <button id="signature-warning-continue" class="action-button primary">Continue</button>
+            </div>
+        </div>
+    </div>
+
+    <!-- Fill Modal (Legacy - can be removed later) -->
     <div id="fill-modal" class="modal-container hidden">
         <div class="modal-content">
             <span class="close-fill-modal-button">&times;</span>
             <h2 id="fill-modal-title">Fill Bundle</h2>
             <div id="fill-modal-body">
-                <p>Select targets to build and add to the bundle:</p>
+                <p>Select the targets you want to build:</p>
                 <div id="fill-targets-list"></div>
-                <button id="start-fill-button" class="action-button">Start Fill</button>
+                <button id="start-fill-button">Start Fill</button>
             </div>
             <div id="fill-progress-view" style="display: none;">
-                <h3>Fill Progress:</h3>
                 <div id="fill-progress-list"></div>
             </div>
         </div>
diff --git a/electron/renderer.js b/electron/renderer.js
index d2edd7b..8c75d26 100644
--- a/electron/renderer.js
+++ b/electron/renderer.js
@@ -26,6 +26,12 @@ const saveOptionsModal = document.getElementById('save-options-modal');
 const overwriteBundleBtn = document.getElementById('overwrite-bundle-btn');
 const saveAsNewBtn = document.getElementById('save-as-new-btn');
 
+// Signature warning modal elements
+const signatureWarningModal = document.getElementById('signature-warning-modal');
+const signatureWarningCancel = document.getElementById('signature-warning-cancel');
+const signatureWarningContinue = document.getElementById('signature-warning-continue');
+let pendingOperation = null; // Store the operation to execute after warning confirmation
+
 // Fill tab elements
 const fillTabLink = document.getElementById('fill-tab-link');
 const loadFillableTargetsBtn = document.getElementById('load-fillable-targets-btn');
@@ -117,6 +123,20 @@ function setupEventListeners() {
   overwriteBundleBtn.addEventListener('click', () => handleSaveMetadata(false));
   saveAsNewBtn.addEventListener('click', () => handleSaveMetadata(true));
   
+  // Signature warning modal event listeners
+  signatureWarningCancel.addEventListener('click', () => {
+    signatureWarningModal.classList.add('hidden');
+    pendingOperation = null;
+  });
+  
+  signatureWarningContinue.addEventListener('click', () => {
+    signatureWarningModal.classList.add('hidden');
+    if (pendingOperation) {
+      pendingOperation();
+      pendingOperation = null;
+    }
+  });
+  
   // Load fillable targets button
   loadFillableTargetsBtn.addEventListener('click', async () => {
     await loadFillableTargets();
@@ -185,6 +205,35 @@ function setupEventListeners() {
     fillTargetsContent.classList.add('hidden');
   }
 
+  // Check if bundle is signed and show warning before bundle-modifying operations
+  function checkSignatureAndWarn(operation, operationName = 'operation') {
+    console.log('checkSignatureAndWarn called for:', operationName);
+    console.log('currentBundle:', currentBundle);
+    
+    // Check if current bundle has a valid signature
+    const isSigned = currentBundle && 
+                    currentBundle.report && 
+                    currentBundle.report.signature && 
+                    currentBundle.report.signature.status && 
+                    ['TRUSTED', 'UNTRUSTED'].includes(currentBundle.report.signature.status);
+    
+    console.log('Bundle signature status:', currentBundle?.report?.signature?.status);
+    console.log('isSigned:', isSigned);
+    
+    if (isSigned) {
+      // Bundle is signed, show warning modal
+      console.log('Bundle is signed, showing warning modal');
+      pendingOperation = operation;
+      signatureWarningModal.classList.remove('hidden');
+      return false; // Don't execute operation immediately
+    } else {
+      // Bundle is not signed, execute operation directly
+      console.log('Bundle is not signed, executing operation directly');
+      operation();
+      return true; // Operation executed
+    }
+  }
+
   // Old modal code removed - now using tab-based interface
 
   // Create modern table-based interface for fillable targets
@@ -290,25 +339,28 @@ function setupEventListeners() {
         selectedTargets[pluginName].push(target);
       });
 
-      // Hide target selection and show progress
-      fillTargetsContent.classList.add('hidden');
-      fillProgressContainer.classList.remove('hidden');
-      populateFillProgress(selectedTargets);
+      // Check for signature and warn before starting fill process
+      checkSignatureAndWarn(async () => {
+        // Hide target selection and show progress
+        fillTargetsContent.classList.add('hidden');
+        fillProgressContainer.classList.remove('hidden');
+        populateFillProgress(selectedTargets);
 
-      const result = await ipcRenderer.invoke('fill-bundle', { 
-        bundlePath: currentBundlePath, 
-        targetsToBuild: selectedTargets 
-      });
+        const result = await ipcRenderer.invoke('fill-bundle', { 
+          bundlePath: currentBundlePath, 
+          targetsToBuild: selectedTargets 
+        });
 
-      if (!result.success) {
-        const errorItem = document.createElement('div');
-        errorItem.className = 'progress-item';
-        errorItem.innerHTML = `
-          <span class="progress-status failure">Error</span>
-          <span>Fill process failed: ${result.error}</span>
-        `;
-        fillProgressContent.appendChild(errorItem);
-      }
+        if (!result.success) {
+          const errorItem = document.createElement('div');
+          errorItem.className = 'progress-item';
+          errorItem.innerHTML = `
+            <span class="progress-status failure">Error</span>
+            <span>Fill process failed: ${result.error}</span>
+          `;
+          fillProgressContent.appendChild(errorItem);
+        }
+      }, 'fill bundle');
     });
   }
 
@@ -723,7 +775,24 @@ function updateSaveButtonVisibility() {
 
 // Show save options modal
 function showSaveOptionsModal() {
-  if (!currentBundlePath || !hasUnsavedChanges) return;
+  if (!hasUnsavedChanges) {
+    return;
+  }
+  
+  // Check if bundle is signed and show warning banner
+  const signatureWarningSection = document.getElementById('signature-warning-section');
+  const isSigned = currentBundle && 
+                  currentBundle.report && 
+                  currentBundle.report.signature && 
+                  currentBundle.report.signature.status && 
+                  ['TRUSTED', 'UNTRUSTED'].includes(currentBundle.report.signature.status);
+  
+  if (isSigned) {
+    signatureWarningSection.classList.remove('hidden');
+  } else {
+    signatureWarningSection.classList.add('hidden');
+  }
+  
   saveOptionsModal.classList.remove('hidden');
 }
 
diff --git a/electron/styles.css b/electron/styles.css
index 22fd5a1..ff0cf47 100644
--- a/electron/styles.css
+++ b/electron/styles.css
@@ -499,6 +499,7 @@ body {
 
 .fill-target-checkbox {
     margin-right: 8px;
+    border-color: var(--primary-hover);
 }
 
 .fill-actions {
@@ -578,6 +579,85 @@ body {
     color: #991b1b;
 }
 
+/* Signature Warning Modal */
+#signature-warning-modal .modal-content {
+    max-width: 500px;
+}
+
+#signature-warning-modal h2 {
+    color: #f59e0b;
+    margin-bottom: 16px;
+    display: flex;
+    align-items: center;
+    gap: 8px;
+}
+
+.warning-content {
+    margin-bottom: 24px;
+}
+
+.warning-content p {
+    margin-bottom: 12px;
+    line-height: 1.5;
+}
+
+.warning-content ul {
+    margin: 12px 0;
+    padding-left: 24px;
+}
+
+.warning-content li {
+    margin-bottom: 6px;
+    line-height: 1.4;
+}
+
+.modal-actions {
+    display: flex;
+    gap: 12px;
+    justify-content: flex-end;
+}
+
+.modal-actions button {
+    padding: 10px 20px;
+    border: none;
+    border-radius: 6px;
+    cursor: pointer;
+    font-size: 14px;
+    font-weight: 600;
+    transition: background-color 0.2s;
+}
+
+/* Signature Warning Banner in Save Modal */
+.signature-warning-section {
+    margin-bottom: 20px;
+}
+
+.warning-banner {
+    display: flex;
+    align-items: flex-start;
+    gap: 12px;
+    padding: 16px;
+    background-color: #fef3c7;
+    border: 1px solid #f59e0b;
+    border-radius: 8px;
+    margin-bottom: 16px;
+}
+
+.warning-icon {
+    font-size: 20px;
+    flex-shrink: 0;
+    margin-top: 2px;
+}
+
+.warning-text {
+    line-height: 1.5;
+    color: #92400e;
+}
+
+.warning-text strong {
+    color: #78350f;
+}
+
 /* Save Options Modal */
 .save-options {
     display: flex;