Made a call today to the 855 number and had a little chat with a cr,so the suggestion was to do a reset,sync and drag the side loaded books back
using ADE.
I hear the code is open source,so that would be worth looking into.
There's too many good books to read to spend time chasing bugs down the yellow brick road.
By Phone
Kobo Help Line, United States and Canada:
1-866-204-4714-not working
1-855-732-3662-working
(8am - 12am EST)
Here is the website.
http://www.kobobooks.com/help