### 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)
if (!p_only_imported_files) {
		if (!source_file.is_empty() && source_file != p_path) {
			return true; 
		}
		if (source_md5.is_empty()) {
			return true; 
		}
		String md5 = FileAccess::get_md5(p_path);
		if (md5 != source_md5) {
			return true;
		}
		if (dest_files.size() && !dest_md5.is_empty()) {
			md5 = FileAccess::get_multiple_md5(dest_files);
			if (md5 != dest_md5) {
				return true;
			}
		}
	}
	return false; 
}
bool EditorFileSystem::_scan_import_support(Vector<String> reimports) {
	if (import_support_queries.size() == 0) {
		return false;
	}
	HashMap<String, int> import_support_test;
	Vector<bool> import_support_tested;
	import_support_tested.resize(import_support_queries.size());
	for (int i = 0; i < import_support_queries.size(); i++) {
		import_support_tested.write[i] = false;