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Hi, we also run across this issue when trying to clear up old family table files. We have exploded many family tables in the past, I'm glad I did most of them before we migrated to Windchill!
I've also had a PTC tech support case last year, attempting to remove instances, though I'm usually trying to purge non-latest instead of latest as mentioned by John.
Anyway, our temporary 'solution' is to move unwanted to files to a context that has no public access so they're essentially hidden from everyday users.
Edwin