### 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)
/** This hack exists because of the EditorProgress nature
				 *  of processing events recursively. This needs to be rewritten
				 *  at some point entirely, but in the meantime the following
				 *  hack prevents deadlock on import.
				 */
				static bool prevent_recursive_process_hack = false;
				if (prevent_recursive_process_hack) {
					break;
				}
				prevent_recursive_process_hack = true;
				bool done_importing = false;
				if (scanning_changes) {
					if (scanning_changes_done) {
						set_process(false);
						if (thread_sources.is_started()) {
							thread_sources.wait_to_finish();
						}
						bool changed = _update_scan_actions();
						_update_pending_script_classes();
						if (changed) {
							emit_signal(SNAME("filesystem_changed"));
						}
						emit_signal(SNAME("sources_changed"), sources_changed.size() > 0);
						first_scan = false;
						scanning_changes = false; 
						done_importing = true;
					}
				} else if (!scanning && thread.is_started()) {
					set_process(false);
					if (filesystem) {