### 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)
EditorFileSystemDirectory *fs = nullptr;
	int cpos = -1;
	if (!_find_file(p_file, &fs, cpos)) {
		return "";
	}
	return fs->files[cpos]->type;
}
EditorFileSystemDirectory *EditorFileSystem::find_file(const String &p_file, int *r_index) const {
	if (!filesystem || scanning) {
		return nullptr;
	}
	EditorFileSystemDirectory *fs = nullptr;
	int cpos = -1;
	if (!_find_file(p_file, &fs, cpos)) {
		return nullptr;
	}
	if (r_index) {
		*r_index = cpos;
	}
	return fs;
}
EditorFileSystemDirectory *EditorFileSystem::get_filesystem_path(const String &p_path) {
	if (!filesystem || scanning) {
		return nullptr;
	}
	String f = ProjectSettings::get_singleton()->localize_path(p_path);
	if (!f.begins_with("res://")) {
		return nullptr;
	}