### 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)
while (sources.has(next_source_id)) {
		next_source_id = (next_source_id + 1) % 1073741824; 
	};
}
int TileSet::add_source(Ref<TileSetSource> p_tile_set_source, int p_atlas_source_id_override) {
	ERR_FAIL_COND_V(!p_tile_set_source.is_valid(), TileSet::INVALID_SOURCE);
	ERR_FAIL_COND_V_MSG(p_atlas_source_id_override >= 0 && (sources.has(p_atlas_source_id_override)), TileSet::INVALID_SOURCE, vformat("Cannot create TileSet atlas source. Another atlas source exists with id %d.", p_atlas_source_id_override));
	ERR_FAIL_COND_V_MSG(p_atlas_source_id_override < 0 && p_atlas_source_id_override != TileSet::INVALID_SOURCE, TileSet::INVALID_SOURCE, vformat("Provided source ID %d is not valid. Negative source IDs are not allowed.", p_atlas_source_id_override));
	int new_source_id = p_atlas_source_id_override >= 0 ? p_atlas_source_id_override : next_source_id;
	sources[new_source_id] = p_tile_set_source;
	source_ids.push_back(new_source_id);
	source_ids.sort();
	TileSet *old_tileset = p_tile_set_source->get_tile_set();
	if (old_tileset != this && old_tileset != nullptr) {
		
		old_tileset->remove_source_ptr(p_tile_set_source.ptr());
	}
	p_tile_set_source->set_tile_set(this);
	_compute_next_source_id();
	sources[new_source_id]->connect_changed(callable_mp(this, &TileSet::_source_changed));
	terrains_cache_dirty = true;
	emit_changed();
	return new_source_id;
}
void TileSet::remove_source(int p_source_id) {