I went through and checked all of my Kobo and Sony books. I had some of my Sony books still in my Kobo library, including one that didn't transfer back in 2014.
I managed to re-add over 100 books with the “You already own this item, but have removed it from your library. You can add it back using the button below.” (which Kobo removed not me
). Such fun
But there were some they wanted to me to rebuy and others no longer for sale. Not all of my missing books were Sony transfers. Some were purchased at Kobo. But I'm not going to bother arguing with them over the missing books from my library since they're in Calibre and I have my backups. Dealing with their customer service isn't worth the headache.