### 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)
ERR_FAIL_COND(import_support_queries.find(p_query) != -1);
	import_support_queries.push_back(p_query);
}
void EditorFileSystem::remove_import_format_support_query(Ref<EditorFileSystemImportFormatSupportQuery> p_query) {
	import_support_queries.erase(p_query);
}
EditorFileSystem::EditorFileSystem() {
	ResourceLoader::import = _resource_import;
	reimport_on_missing_imported_files = GLOBAL_GET("editor/import/reimport_missing_imported_files");
	singleton = this;
	filesystem = memnew(EditorFileSystemDirectory); 
	filesystem->parent = nullptr;
	new_filesystem = nullptr;
	
	Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
	using_fat32_or_exfat = (da->get_filesystem_type() == "FAT32" || da->get_filesystem_type() == "exFAT");
	scan_total = 0;
	MessageQueue::get_singleton()->push_callable(callable_mp(ResourceUID::get_singleton(), &ResourceUID::clear)); 
	ResourceSaver::set_get_resource_id_for_path(_resource_saver_get_resource_id_for_path);
}
EditorFileSystem::~EditorFileSystem() {
	ResourceSaver::set_get_resource_id_for_path(nullptr);
}