Importing the notes with the same ID is not really an option, as it would create more problems than it would solve. For example, it means that if you import a note it would overwrite any existing one - but what if that's not what you want? What if you just want to restore an old version of the note and compare it to the existing one. Also if you delete a note, then restore it via backup, then sync, I think it would still delete it on the sync target because the app doesn't support deleted notes reappearing out of the blue.
In general you don't want backup set to refer to outside data because that data might have changed or be gone. That's why I think the ideal solution would be to package all the linked notes in the JEX archive,
