I have spent a lot of time investigating this issue. I've worked with a large number of different backups, some as large as 1.6GB. I've made some minor fixes that I didn't think would entirely fix the problem, but since then, I have been completely unable to reproduce a case where I backup or restore a file, and files are missing afterward. I'm going to ask for people to test this again after the next update to see if they are experiencing any more issues. I'm hoping that maybe the problem is fixed.
Mike
Mike