### 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)
found_uid = true;
			} else if (!p_only_imported_files) {
				if (assign == "source_file") {
					source_file = value;
				} else if (assign == "dest_files") {
					dest_files = value;
				}
			}
		} else if (next_tag.name != "remap" && next_tag.name != "deps") {
			break;
		}
	}
	if (importer_name == "keep") {
		return false; 
	}
	if (!found_uid) {
		return true; 
	}
	Ref<ResourceImporter> importer = ResourceFormatImporter::get_singleton()->get_importer_by_name(importer_name);
	if (importer.is_null()) {
		return true; 
	}
	if (importer->get_format_version() > version) {
		return true; 
	}
	
	String base_path = ResourceFormatImporter::get_singleton()->get_import_base_path(p_path);
	Ref<FileAccess> md5s = FileAccess::open(base_path + ".md5", FileAccess::READ, &err);
	if (md5s.is_null()) { 
		return true;