### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(tile_set.is_null());
	ERR_FAIL_COND(p_pattern.is_null());
	TypedArray<Vector2i> used_cells = p_pattern->get_used_cells();
	for (int i = 0; i < used_cells.size(); i++) {
		Vector2i coords = tile_map_node->map_pattern(p_position, used_cells[i], p_pattern);
		set_cell(coords, p_pattern->get_cell_source_id(used_cells[i]), p_pattern->get_cell_atlas_coords(used_cells[i]), p_pattern->get_cell_alternative_tile(used_cells[i]));
	}
}
void TileMapLayer::set_cells_terrain_connect(TypedArray<Vector2i> p_cells, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	ERR_FAIL_INDEX(p_terrain_set, tile_set->get_terrain_sets_count());
	Vector<Vector2i> cells_vector;
	HashSet<Vector2i> painted_set;
	for (int i = 0; i < p_cells.size(); i++) {
		cells_vector.push_back(p_cells[i]);
		painted_set.insert(p_cells[i]);
	}
	HashMap<Vector2i, TileSet::TerrainsPattern> terrain_fill_output = terrain_fill_connect(cells_vector, p_terrain_set, p_terrain, p_ignore_empty_terrains);
	for (const KeyValue<Vector2i, TileSet::TerrainsPattern> &kv : terrain_fill_output) {
		if (painted_set.has(kv.key)) {
			
			TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
			set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
		} else {