### 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)
terrain_meshes.clear();
	terrain_peering_bits_meshes.clear();
	per_terrain_pattern_tiles.clear();
	terrains_cache_dirty = true;
	
	navigation_layers.clear();
	custom_data_layers.clear();
	custom_data_layers_by_name.clear();
	
	source_level_proxies.clear();
	coords_level_proxies.clear();
	alternative_level_proxies.clear();
#ifndef DISABLE_DEPRECATED
	for (const KeyValue<int, CompatibilityTileData *> &E : compatibility_data) {
		memdelete(E.value);
	}
	compatibility_data.clear();
#endif 
	while (!source_ids.is_empty()) {
		remove_source(source_ids[0]);
	}
	tile_shape = TILE_SHAPE_SQUARE;
	tile_layout = TILE_LAYOUT_STACKED;
	tile_offset_axis = TILE_OFFSET_AXIS_HORIZONTAL;
	tile_size = Size2i(16, 16);
}
const Vector2i TileSetSource::INVALID_ATLAS_COORDS = Vector2i(-1, -1);
const int TileSetSource::INVALID_TILE_ALTERNATIVE = -1;
#ifndef DISABLE_DEPRECATED
void TileSet::_compatibility_conversion() {