### 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)
}
	}
	
	for (int terrain_set = 0; terrain_set < get_terrain_sets_count(); terrain_set++) {
		for (int terrain = 0; terrain < get_terrains_count(terrain_set); terrain++) {
			Ref<Image> dst_image;
			dst_image.instantiate();
			if (counts[terrain_set][terrain].count > 0) {
				
				Ref<Texture2D> src_texture = counts[terrain_set][terrain].texture;
				ERR_FAIL_COND_V(src_texture.is_null(), output);
				Ref<Image> src_image = src_texture->get_image();
				ERR_FAIL_COND_V(src_image.is_null(), output);
				Rect2i region = counts[terrain_set][terrain].region;
				dst_image->initialize_data(region.size.x, region.size.y, false, src_image->get_format());
				dst_image->blit_rect(src_image, region, Point2i());
				dst_image->convert(Image::FORMAT_RGBA8);
				dst_image->resize(p_size.x, p_size.y, Image::INTERPOLATE_NEAREST);
			} else {
				dst_image->initialize_data(1, 1, false, Image::FORMAT_RGBA8);
				dst_image->set_pixel(0, 0, get_terrain_color(terrain_set, terrain));
			}
			Ref<ImageTexture> icon = ImageTexture::create_from_image(dst_image);
			icon->set_size_override(p_size);
			output.write[terrain_set].write[terrain] = icon;
		}
	}
	return output;
}
void TileSet::_source_changed() {