### 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)
ClassDB::bind_method(D_METHOD("get_filesystem"), &EditorFileSystem::get_filesystem);
	ClassDB::bind_method(D_METHOD("is_scanning"), &EditorFileSystem::is_scanning);
	ClassDB::bind_method(D_METHOD("get_scanning_progress"), &EditorFileSystem::get_scanning_progress);
	ClassDB::bind_method(D_METHOD("scan"), &EditorFileSystem::scan);
	ClassDB::bind_method(D_METHOD("scan_sources"), &EditorFileSystem::scan_changes);
	ClassDB::bind_method(D_METHOD("update_file", "path"), &EditorFileSystem::update_file);
	ClassDB::bind_method(D_METHOD("get_filesystem_path", "path"), &EditorFileSystem::get_filesystem_path);
	ClassDB::bind_method(D_METHOD("get_file_type", "path"), &EditorFileSystem::get_file_type);
	ClassDB::bind_method(D_METHOD("reimport_files", "files"), &EditorFileSystem::reimport_files);
	ADD_SIGNAL(MethodInfo("filesystem_changed"));
	ADD_SIGNAL(MethodInfo("script_classes_updated"));
	ADD_SIGNAL(MethodInfo("sources_changed", PropertyInfo(Variant::BOOL, "exist")));
	ADD_SIGNAL(MethodInfo("resources_reimported", PropertyInfo(Variant::PACKED_STRING_ARRAY, "resources")));
	ADD_SIGNAL(MethodInfo("resources_reload", PropertyInfo(Variant::PACKED_STRING_ARRAY, "resources")));
}
void EditorFileSystem::_update_extensions() {