Fix modifying header height

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: