### 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)
}
	VariantParser::StreamFile md5_stream;
	md5_stream.f = md5s;
	while (true) {
		assign = Variant();
		next_tag.fields.clear();
		next_tag.name = String();
		err = VariantParser::parse_tag_assign_eof(&md5_stream, lines, error_text, next_tag, assign, value, nullptr, true);
		if (err == ERR_FILE_EOF) {
			break;
		} else if (err != OK) {
			ERR_PRINT("ResourceFormatImporter::load - '" + p_path + ".import.md5:" + itos(lines) + "' error '" + error_text + "'.");
			return false; 
		}
		if (!assign.is_empty()) {
			if (!p_only_imported_files) {
				if (assign == "source_md5") {
					source_md5 = value;
				} else if (assign == "dest_md5") {
					dest_md5 = value;
				}
			}
		}
	}
	
	for (const String &E : to_check) {
		if (!FileAccess::exists(E)) {
			return true;
		}
	}