diff --git a/reading_annotations.py b/reading_annotations.py
index c11b29b..fe9acde 100644
--- a/reading_annotations.py
+++ b/reading_annotations.py
@@ -255,7 +255,7 @@ def apply_actions_and_regenerate(root_dir, data, student_id, actions, notes_laye
         (base_img, _, _) = annotating.make_base_image(pdf_path)
 
         # Compose uses the result object we modified in step 1
-        final_img, _ = annotating.compose_label_image(
+        final_img, new_header_h = annotating.compose_label_image(
             base_img, label, content['result'], content['coordinates'][0],
             with_error=False
         )
@@ -264,7 +264,18 @@ def apply_actions_and_regenerate(root_dir, data, student_id, actions, notes_laye
 
         # Overlay manual notes
         if has_notes:
-            final_img.paste(sub_note, (0, 0), mask=sub_note)
+            old_header_h = int(img_info.get("header_height", 0))
+            w, h = sub_note.size
+
+            # 1. Paste header ink at the top
+            if old_header_h > 0:
+                header_crop = sub_note.crop((0, 0, w, min(h, old_header_h)))
+                final_img.paste(header_crop, (0, 0), mask=header_crop)
+
+            # 2. Paste student-content ink at the new header height
+            if h > old_header_h:
+                body_crop = sub_note.crop((0, old_header_h, w, h))
+                final_img.paste(body_crop, (0, new_header_h), mask=body_crop)
 
         # C. Save individual file if Modified (Dirty logic or visual notes)
         if (label in dirty_labels) or has_notes:
diff --git a/reading_grouped_annotations.py b/reading_grouped_annotations.py
index af4001f..b74260c 100644
--- a/reading_grouped_annotations.py
+++ b/reading_grouped_annotations.py
@@ -81,7 +81,7 @@ def apply_actions_and_regenerate_grouped(root_dir, data, student_id, actions, la
         (base_img, _, _) = annotating.make_base_image(pdf_path)
 
         # Compose uses the result object we modified in step 1
-        final_img, _ = annotating.compose_label_image(
+        final_img, new_header_h = annotating.compose_label_image(
             base_img, label, content['result'], content['coordinates'][0],
             with_error=False
         )
@@ -91,10 +91,23 @@ def apply_actions_and_regenerate_grouped(root_dir, data, student_id, actions, la
         # Overlay manual notes specific to this label
         has_notes = False
         if label in label_notes:
-            sub_note = label_notes[label]
+            note_info = label_notes[label]
+            sub_note = note_info['img']
+            old_header_h = int(note_info['old_header_h'])
+
             if has_significant_notes(sub_note):
                 has_notes = True
-                final_img.paste(sub_note, (0, 0), mask=sub_note)
+                w, h = sub_note.size
+
+                # 1. Paste header ink at the top
+                if old_header_h > 0:
+                    header_crop = sub_note.crop((0, 0, w, min(h, old_header_h)))
+                    final_img.paste(header_crop, (0, 0), mask=header_crop)
+
+                # 2. Paste student-content ink at the new header height
+                if h > old_header_h:
+                    body_crop = sub_note.crop((0, old_header_h, w, h))
+                    final_img.paste(body_crop, (0, new_header_h), mask=body_crop)
 
         # Save individual file if Modified (Dirty logic or visual notes)
         if (label in dirty_labels) or has_notes:
@@ -205,7 +218,10 @@ if __name__ == "__main__":
                 crop = notes_img.crop((0, hmin, notes_img.width, hmax))
                 # Store it if there are pen marks on it
                 if has_significant_notes(crop):
-                    notes_by_student[sid][lbl] = crop
+                    notes_by_student[sid][lbl] = {
+                        'img': crop,
+                        'old_header_h': img_info.get("header_height", 0)
+                    }
 
     # --- 2. Dispatch data back to students and regenerate ---
     # affected_students = set(actions_by_student.keys()).union(set(notes_by_student.keys()))