OK, I do use Kindle for PC to download my books, then import into Calibre, hoping that Alf's tools work, and then convert. But I have been importing large batches at one time as I've been rebuilding my Calibre library after losing a lot of stuff last year when I made some mistakes in transferring it to my new computer.
Kovid's way of determining exactly which books are affected will be a big help and is exactly what i was hoping to learn. But all the other info you all have posted is a big help as well, as I did not realize that about the AZW3 vs AZW. I will do a few at a time this time around and be more quick to catch any problems.