### 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)
TILEMAP_CALL_FOR_LAYER_V(p_layer, RID(), get_navigation_map);
}
void TileMap::set_collision_animatable(bool p_enabled) {
	if (collision_animatable == p_enabled) {
		return;
	}
	collision_animatable = p_enabled;
	_update_notify_local_transform();
	set_physics_process_internal(p_enabled);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_COLLISION_ANIMATABLE);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
}
bool TileMap::is_collision_animatable() const {
	return collision_animatable;
}
void TileMap::set_collision_visibility_mode(TileMap::VisibilityMode p_show_collision) {
	if (collision_visibility_mode == p_show_collision) {
		return;
	}
	collision_visibility_mode = p_show_collision;
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_COLLISION_VISIBILITY_MODE);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
}
TileMap::VisibilityMode TileMap::get_collision_visibility_mode() {