I feel your pain, literally.
I have also had various problems with my data disappearing from the Nook Color (not just books, but music and pictures). I also finally realized that the SD card did not have this problem. Now everything is on the SD card except B&N stuff.
The problem between Adobe and Nook also hit me. Stupidly I forgot to back up my apps, including my calendar app which has become my default when I am not at home. I am still recovering from that.
Also, I keep most of my stuff either in the B&N cloud or in my Calibre library. I have fewer than 20 books in my Nook. I use Calibre for most of my side-loading. I only use Adobe for library books. If I could figure out how to avoid Adobe for that, I would be happy.
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