### Godot version

v4.1.beta.custom_build [72b59325c]

### System information

Windows 10, Vulkan

### Issue description

This has been plaguing me for a while in my main project. I can only partially reproduce it in a MRP:
When placing a binary mesh resource imported from a .glb file into a MeshInstance3D, it will be gone upon restart. It doesn't seem to happen to every resource, but I've had MIs that were fine and then start doing it out of nowhere.
I thought it was going to be related to materials due to things like https://github.com/godotengine/godot/issues/77007 but I can reliably trigger it with the steps listed below.
I have done limited testing on .tres files because I usually use .res for size/performance, but in the MRP .tres doesn't seem to trigger it, so perhaps it doesn't affect those.

Note on the Steps to reproduce: you have to delete the test_cube.res and redo the steps to trigger the bug again, but in my main project the affected resources always disappear.

### Steps to reproduce

1. Double click test_cube.glb
2. Click the mesh (test_cube_Cube_097), set save to file path as: res://test_cube.res
3. Make sure to click the little folder icon and then Save (this seems to make it consistent to proc)
4. Press Reimport
5. Drag the test_cube.res to the Mesh slot of the MeshInstance3D
6. Ctrl+s to save
7. Project -> Reload current project
8. Mesh is no longer in the MeshInstance3D

### Minimal reproduction project

[binary res bug.zip](https://github.com/godotengine/godot/files/11681009/binary.res.bug.zip)
valid_extensions.clear();
	import_extensions.clear();
	textfile_extensions.clear();
	List<String> extensionsl;
	ResourceLoader::get_recognized_extensions_for_type("", &extensionsl);
	for (const String &E : extensionsl) {
		valid_extensions.insert(E);
	}
	const Vector<String> textfile_ext = ((String)(EDITOR_GET("docks/filesystem/textfile_extensions"))).split(",", false);
	for (const String &E : textfile_ext) {
		if (valid_extensions.has(E)) {
			continue;
		}
		valid_extensions.insert(E);
		textfile_extensions.insert(E);
	}
	extensionsl.clear();
	ResourceFormatImporter::get_singleton()->get_recognized_extensions(&extensionsl);
	for (const String &E : extensionsl) {
		import_extensions.insert(E);
	}
}
void EditorFileSystem::add_import_format_support_query(Ref<EditorFileSystemImportFormatSupportQuery> p_query) {