### 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)
return z_index;
}
void TileMapLayer::set_navigation_enabled(bool p_enabled) {
	if (navigation_enabled == p_enabled) {
		return;
	}
	navigation_enabled = p_enabled;
	dirty.flags[DIRTY_FLAGS_LAYER_NAVIGATION_ENABLED] = true;
	tile_map_node->queue_internal_update();
	tile_map_node->emit_signal(CoreStringNames::get_singleton()->changed);
}
bool TileMapLayer::is_navigation_enabled() const {
	return navigation_enabled;
}
void TileMapLayer::set_navigation_map(RID p_map) {
	ERR_FAIL_COND_MSG(!tile_map_node->is_inside_tree(), "A TileMap navigation map can only be changed while inside the SceneTree.");
	navigation_map = p_map;
	uses_world_navigation_map = p_map == tile_map_node->get_world_2d()->get_navigation_map();
}
RID TileMapLayer::get_navigation_map() const {
	if (navigation_map.is_valid()) {
		return navigation_map;
	}
	return RID();
}
void TileMapLayer::fix_invalid_tiles() {