NookGlolight 3 BNRV 520 loses books from library

[sdean7855]

I had some 150 books in it, which represents about 5.5GB free out of 6.3GB total. I started reading books by one author wherein I had some 6 books by her, now I only see 2 of them. This is a chronic problem that's happened before. I thought it was that I had too many books, so I cut down the library from 500+ to 150. Everything was there when I began reading, now 4 of the 6 books are missing. Less books didn't help.
1) Is this a known problem of the Nook GL 3 , BNRV 520? Is there a fix?
2) Is there some way with Calibre to regen the directory structure short of wiping the reader and re-downloading everything?
3) Would it work better with Aldiko if rooted? That works fine on my Samsung Note4, which also runs KitKat. If so, can someone point me to an idiot's guide to rooting it?