### Godot version

4.1 rc3

### System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

### Issue description

This™
![image](https://github.com/godotengine/godot/assets/2223172/cb33110f-a5b0-400a-951f-3fa425f05714)

It can still happen, but it's more difficult to trigger.

### Steps to reproduce

1. Create a new scene with a Control node
2. Add Theme to the Control
3. Open Theme Editor
4. Clear the `theme` property in Control
5. Save, with Theme Editor opened
6. Restart

### Minimal reproduction project

N/A
for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
					if (editor_data.get_scene_path(i) == p_file && i != scene_idx) {
						same_open_scene = true;
					}
				}
				if (same_open_scene) {
					show_warning(TTR("Can't overwrite scene that is still open!"));
					return;
				}
				save_default_environment();
				_save_scene_with_preview(p_file, scene_idx);
				_add_to_recent_scenes(p_file);
				save_editor_layout_delayed();
				if (scene_idx != -1) {
					_discard_changes();
				}
			}
		} break;
		case FILE_SAVE_AND_RUN: {
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				save_default_environment();
				_save_scene_with_preview(p_file);
				project_run_bar->play_custom_scene(p_file);
			}
		} break;
		case FILE_SAVE_AND_RUN_MAIN_SCENE: {
			ProjectSettings::get_singleton()->set("application/run/main_scene", p_file);
			ProjectSettings::get_singleton()->save();
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				save_default_environment();