Although it might annoy some users, a quick work-around might be to add a tag to the file. Tags on files/folders don't go away when you move or rename the file.

Although it might annoy some users, a quick work-around might be to add a tag to the file. Tags on files/folders don't go away when you move or rename the file. Something like, "ghostnote:<ID>" where ID is some internal reference to the associated note. In fact... using this method you wouldn't have to store the URLs of files/folders at all.