### 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 (first_scan || 
			scanning || scanning_changes || thread.is_started()) {
		scan_changes_pending = true;
		set_process(true);
		return;
	}
	_update_extensions();
	sources_changed.clear();
	scanning_changes = true;
	scanning_changes_done = false;
	if (!use_threads) {
		if (filesystem) {
			EditorProgressBG pr("sources", TTR("ScanSources"), 1000);
			ScanProgress sp;
			sp.progress = &pr;
			sp.hi = 1;
			sp.low = 0;
			scan_total = 0;
			_scan_fs_changes(filesystem, sp);
			bool changed = _update_scan_actions();
			_update_pending_script_classes();
			if (changed) {
				emit_signal(SNAME("filesystem_changed"));
			}
		}
		scanning_changes = false;
		scanning_changes_done = true;
		emit_signal(SNAME("sources_changed"), sources_changed.size() > 0);
	} else {
		ERR_FAIL_COND(thread_sources.is_started());