### 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 next_source_id;
}
void TileSet::_update_terrains_cache() {
	if (terrains_cache_dirty) {
		
		per_terrain_pattern_tiles.resize(terrain_sets.size());
		for (RBMap<TileSet::TerrainsPattern, RBSet<TileMapCell>> &tiles : per_terrain_pattern_tiles) {
			tiles.clear();
		}
		for (const KeyValue<int, Ref<TileSetSource>> &kv : sources) {
			Ref<TileSetSource> source = kv.value;
			Ref<TileSetAtlasSource> atlas_source = source;
			if (atlas_source.is_valid()) {
				for (int tile_index = 0; tile_index < source->get_tiles_count(); tile_index++) {
					Vector2i tile_id = source->get_tile_id(tile_index);
					for (int alternative_index = 0; alternative_index < source->get_alternative_tiles_count(tile_id); alternative_index++) {
						int alternative_id = source->get_alternative_tile_id(tile_id, alternative_index);
						
						TileData *tile_data = atlas_source->get_tile_data(tile_id, alternative_id);
						int terrain_set = tile_data->get_terrain_set();
						if (terrain_set >= 0) {
							TileMapCell cell;
							cell.source_id = kv.key;
							cell.set_atlas_coords(tile_id);
							cell.alternative_tile = alternative_id;
							TileSet::TerrainsPattern terrains_pattern = tile_data->get_terrains_pattern();
							
							if (terrains_pattern.get_terrain() >= 0) {