you shouldn't delete par2 or data files yourself since UE doesn't track changes in the directory automatically (it could but i didn't go into this direction).
there is an option to synchronize files in the context menu->advanced, "reload exact files" option to synchronize completely it will also cover the case when the files changed. the option works on selected items since it scans all related files in e.g. par2 set - all its par2 files and all data files which are in the set. it was added in v2.1
if you only deleted files you can use context menu->advanced->synchronize files, it will take care of deleted files only, it doesn't scan files so it is done for the whole unpack pane content. this one was from the beginning, v2.0.
just i can run in limited length after users changing, renaming, deleting files, at certain point it should be user responsibility, say if to pour acid on the motherboard UE will stop working for sure
what i did in UE i added options to synchronize files to cover all cases so there is everything needed, but "reload exact files" is a manual option and the "synchronize files" option is also performed every time when you launch UE (so deleted files are handled on every start) and in addition you can invoke it in the middle of the session as well. e.g. if you change a byte or two in outlook express database inbox.dbx file or it changed because of sudden shutdown when you run outlook express next time you may well lose all inbox emails with shrinked file and there is no option to repair that
if you didn't delete any files and you see verification failed try to do repair several times (select the par2 set and invoke "repair" from the context menu). if repair succeeds it means faulty RAM (so better you run memory tests to find the faulty stick) if it doesn't - then invoke "reload exact files" (especially if you changed files), try to repair again, if repair doesn't succeed let me know what was the post, but what i had in the past only one case which was faulty RAM, then you should see the same with quickpar as well rarely, UE is using also system file cache for repair to make things faster so if RAM is not well the probability of verification error is maybe somewhat higher in UE, but not using the cache makes things much slower, sometimes 2 times difference in repair time in my test repairs when i was checking which method is the optimal.