I had about half of my Sony books still in my Kobo library. Most of the ones I was missing had a message “You already own this item, but have removed it from your library. You can add it back using the button below.” Only I hadn’t removed them from the library, Kobo did during this latest “update.” I was able to restore over 100 of them.
There were some no longer for sale at Kobo (including two of my Nalini Singh SD books). And some they want to charge me to buy again (I don’t think so!). A few I understand because they have different ISBNs, but most of them don’t
What’s really strange as there is a book which was not transferred from Sony to Kobo back in March 2014 that I was told by Kobo was unavailable that now does appear in my Kobo account. I don’t think I will ever figure Kobo out.
Not all of my missing books were Sony transfers. Some were purchased at Kobo. But I'm not going to bother arguing with Kobo over them being missing from my library there since they're in Calibre and I have my backups. Dealing with their customer service isn't worth the headache.