### 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)
ERR_FAIL_COND(p_new_source_id < 0);
	ERR_FAIL_COND_MSG(!sources.has(p_source_id), vformat("Cannot change TileSet atlas source ID. No tileset atlas source with id %d.", p_source_id));
	if (p_source_id == p_new_source_id) {
		return;
	}
	ERR_FAIL_COND_MSG(sources.has(p_new_source_id), vformat("Cannot change TileSet atlas source ID. Another atlas source exists with id %d.", p_new_source_id));
	sources[p_new_source_id] = sources[p_source_id];
	sources.erase(p_source_id);
	source_ids.erase(p_source_id);
	source_ids.push_back(p_new_source_id);
	source_ids.sort();
	_compute_next_source_id();
	terrains_cache_dirty = true;
	emit_changed();
}
bool TileSet::has_source(int p_source_id) const {
	return sources.has(p_source_id);
}
Ref<TileSetSource> TileSet::get_source(int p_source_id) const {
	ERR_FAIL_COND_V_MSG(!sources.has(p_source_id), nullptr, vformat("No TileSet atlas source with id %d.", p_source_id));
	return sources[p_source_id];
}
int TileSet::get_source_count() const {
	return source_ids.size();
}
int TileSet::get_source_id(int p_index) const {