I had no theories because I didn't have time to think about it. First client to have this happen suffered through an early adoption 4.10 upgrade, where I first learned that when you reconvert a company, it wipes out everything in that company's Reports folder. (Labels, lots and lots of LABELS.) Needless to say, just had to get this issue fixed ASAP this time so they'd never know it happened.
So this is the UserUpdatedKey in the CI_Item record? And is it ALL UDFS? Seems like mine was only SOME of the UDFs didn't migrate, for all items.