### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

rs->free(ci);
		}
		q.canvas_items.clear();
		
		for (const KeyValue<Vector2i, RID> &kv : q.occluders) {
			rs->free(kv.value);
		}
		q.occluders.clear();
		
		Ref<Material> prev_material;
		int prev_z_index = 0;
		RID prev_ci;
		
		for (const KeyValue<Vector2, Vector2i> &E_cell : q.local_to_map) {
			TileMapCell c = get_cell(E_cell.value, true);
			TileSetSource *source;
			if (tile_set->has_source(c.source_id)) {
				source = *tile_set->get_source(c.source_id);
				if (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
					continue;
				}
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					
					const TileData *tile_data;
					if (q.runtime_tile_data_cache.has(E_cell.value)) {
						tile_data = q.runtime_tile_data_cache[E_cell.value];
					} else {
						tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
					}