I ended up having to do a full factory reset, which was difficult since my reader was stuck at the Kobo face with the 5 blocks cycling left to right nonstop. This finally worked for me:
1. Hold the power button ON for 15-20 seconds to make sure it is off. All lights at the top should be off.
2. Press and HOLD the light button while turning on the Glo. That should put you into a factory reset if that will solve the problem.
After all books were off the reader, I then noticed all the empty shelves were still there and had to delete them all, but one of them was a duplicate and it seems you can't remove either of them when it happens through normal deletion. But I did what
TechniSol did in this post and it worked without having to edit the database.
Then I put back the firmware I prefer, 2.5.1, and loaded books back onto the reader. And of course, I'm getting the "can't communicate with device" from Calibre at times. Usually disconnecting the reader and restarting Calibre will let me load books though.