Keep empty answers in the final individual outputs.

tests/test_annotation_modifications.py

@@ -115,6 +115,29 @@ class ModificationTests(unittest.TestCase):
         self.assertFalse((self.output / "Empty.jpg").exists())
         self.assertFalse(read_json(self.output / "info.json")["Empty"]["not_empty"])
 
+    def test_retained_empty_scan_stays_empty_after_unrelated_edits_and_can_be_replaced(self):
+        self.images["Empty"] = Image.new("RGB", (100, 60), "white")
+        self.heights["Empty"] = 10
+        self.info["Empty"]["present"] = True
+        self.seed()
+        self.apply("Copie43 Ex 1 -> Ex 2|")
+        info = read_json(self.output / "info.json")
+        self.assertTrue((self.output / "Empty.jpg").is_file())
+        self.assertEqual(info["Empty"], self.info["Empty"])
+        with Image.open(self.output / "Concat.jpg") as image:
+            self.assertEqual(image.height, 120 + 180 + 40)
+        self.apply("Copie43 Ex 1 -> Empty")
+        self.assertTrue(read_json(self.output / "info.json")["Empty"]["not_empty"])
+        self.apply()
+        self.assertEqual(read_json(self.output / "info.json")["Empty"], self.info["Empty"])
+
+    def test_removed_body_is_absent_and_not_exported_as_an_empty_scan(self):
+        self.apply("Copie43 Ex 1 x> Ex 2")
+        info = read_json(self.output / "info.json")["Ex 1"]
+        self.assertFalse(info["present"])
+        self.assertFalse(info["not_empty"])
+        self.assertFalse((self.output / "Ex 1.jpg").exists())
+
     def test_invalid_file_does_not_apply_valid_first_instruction(self):
         before = {p.name: p.read_bytes() for p in self.output.iterdir() if p.is_file()}
         with self.assertRaises(CliError):