### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	RenderingServer *rs = RenderingServer::get_singleton();
	
	bool forced_cleanup = in_destructor || !enabled || !tile_map_node->is_inside_tree() || !tile_set.is_valid() || !tile_map_node->is_visible_in_tree();
	if (forced_cleanup) {
		for (KeyValue<Vector2i, Ref<DebugQuadrant>> &kv : debug_quadrant_map) {
			
			Ref<DebugQuadrant> &debug_quadrant = kv.value;
			if (debug_quadrant->canvas_item.is_valid()) {
				rs->free(debug_quadrant->canvas_item);
			}
		}
		debug_quadrant_map.clear();
		_debug_was_cleaned_up = true;
		return;
	}
	
	bool anything_changed = false;
	for (int i = 0; i < DIRTY_FLAGS_MAX; i++) {
		if (dirty.flags[i]) {
			anything_changed = true;
			break;
		}
	}
	
	SelfList<DebugQuadrant>::List dirty_debug_quadrant_list;
	if (_debug_was_cleaned_up || anything_changed) {