### 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)
Error err = config->load(p_files[i] + ".import");
		ERR_CONTINUE(err != OK);
		ERR_CONTINUE(!config->has_section_key("remap", "importer"));
		String file_importer_name = config->get_value("remap", "importer");
		ERR_CONTINUE(file_importer_name.is_empty());
		if (!importer_name.is_empty() && importer_name != file_importer_name) {
			EditorNode::get_singleton()->show_warning(vformat(TTR("There are multiple importers for different types pointing to file %s, import aborted"), p_group_file));
			ERR_FAIL_V(ERR_FILE_CORRUPT);
		}
		ResourceUID::ID uid = ResourceUID::INVALID_ID;
		if (config->has_section_key("remap", "uid")) {
			String uidt = config->get_value("remap", "uid");
			uid = ResourceUID::get_singleton()->text_to_id(uidt);
		}
		uids[p_files[i]] = uid;
		source_file_options[p_files[i]] = HashMap<StringName, Variant>();
		importer_name = file_importer_name;
		if (importer_name == "keep") {
			continue; 
		}
		Ref<ResourceImporter> importer = ResourceFormatImporter::get_singleton()->get_importer_by_name(importer_name);
		ERR_FAIL_COND_V(!importer.is_valid(), ERR_FILE_CORRUPT);
		List<ResourceImporter::ImportOption> options;
		importer->get_import_options(p_files[i], &options);
		
		for (const ResourceImporter::ImportOption &E : options) {
			source_file_options[p_files[i]][E.option.name] = E.default_value;
		}
		if (config->has_section("params")) {
			List<String> sk;