### 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)

ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	if (navigation_map.is_valid()) {
		if (uses_world_navigation_map) {
			
			return;
		}
		NavigationServer2D::get_singleton()->free(navigation_map);
		navigation_map = RID();
	}
}
void TileMapLayer::_navigation_cleanup_quadrant(TileMapQuadrant *p_quadrant) {
	
	ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	for (const KeyValue<Vector2i, Vector<RID>> &E : p_quadrant->navigation_regions) {
		for (int i = 0; i < E.value.size(); i++) {
			RID region = E.value[i];
			if (!region.is_valid()) {
				continue;
			}
			NavigationServer2D::get_singleton()->free(region);
		}
	}
	p_quadrant->navigation_regions.clear();
}
void TileMapLayer::_navigation_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {