### 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)
EditorFileSystemDirectory *fs = nullptr;
	int cpos = -1;
	bool found = _find_file(p_file, &fs, cpos);
	ERR_FAIL_COND_V_MSG(!found, ERR_FILE_NOT_FOUND, "Can't find file '" + p_file + "'.");
	
	HashMap<StringName, Variant> params = p_custom_options;
	String importer_name; 
	if (!p_custom_importer.is_empty()) {
		importer_name = p_custom_importer;
	}
	ResourceUID::ID uid = ResourceUID::INVALID_ID;
	Variant generator_parameters;
	if (p_generator_parameters) {
		generator_parameters = *p_generator_parameters;
	}
	if (FileAccess::exists(p_file + ".import")) {
		
		Ref<ConfigFile> cf;
		cf.instantiate();
		Error err = cf->load(p_file + ".import");
		if (err == OK) {
			if (cf->has_section("params")) {
				List<String> sk;
				cf->get_section_keys("params", &sk);
				for (const String &E : sk) {
					if (!params.has(E)) {
						params[E] = cf->get_value("params", E);
					}