deleted file, not sure it is autoUpdaterSolved

After at least 20 successful version updates over the last couple of years, suddenly it seems like the auto-updater is deleting a file that it has never known about before. That is, I know how wyUpdate works and that - if a file is in one version and not in a later version wyUpdate will delete it. So, I have verified that the file does not exist in any earlier version. 
We have 5 reports this week of our custom .licx file disappearing after applying the latest update, but we are unable to reproduce the error on any internal machines. Is there any way to inspect an update file to see what it is doing?
Although I guess if that was the source of the problem it would fail for everyone...