### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
Dictionary new_dict = p_new_value;
	EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
	for (KeyValue<TileMapCell, Variant> &E : p_previous_values) {
		Vector2i coords = E.key.get_atlas_coords();
		Dictionary old_dict = E.value;
		undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/linear_velocity", coords.x, coords.y, E.key.alternative_tile, physics_layer), old_dict["linear_velocity"]);
		undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/angular_velocity", coords.x, coords.y, E.key.alternative_tile, physics_layer), old_dict["angular_velocity"]);
		Array old_polygon_array = old_dict["polygons"];
		undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygons_count", coords.x, coords.y, E.key.alternative_tile, physics_layer), old_polygon_array.size());
		for (int i = 0; i < old_polygon_array.size(); i++) {
			Dictionary polygon_dict = old_polygon_array[i];
			undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/points", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["points"]);
			undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/one_way", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["one_way"]);
			undo_redo->add_undo_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/one_way_margin", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["one_way_margin"]);
		}
		undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/linear_velocity", coords.x, coords.y, E.key.alternative_tile, physics_layer), new_dict["linear_velocity"]);
		undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/angular_velocity", coords.x, coords.y, E.key.alternative_tile, physics_layer), new_dict["angular_velocity"]);
		Array new_polygon_array = new_dict["polygons"];
		undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygons_count", coords.x, coords.y, E.key.alternative_tile, physics_layer), new_polygon_array.size());
		for (int i = 0; i < new_polygon_array.size(); i++) {
			Dictionary polygon_dict = new_polygon_array[i];
			undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/points", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["points"]);
			undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/one_way", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["one_way"]);
			undo_redo->add_do_property(p_tile_set_atlas_source, vformat("%d:%d/%d/physics_layer_%d/polygon_%d/one_way_margin", coords.x, coords.y, E.key.alternative_tile, physics_layer, i), polygon_dict["one_way_margin"]);
		}
	}
}
void TileDataCollisionEditor::_tile_set_changed() {