How about losing track of Formats?
I know better than to add/remove formats outside of the GUI.
I had a
Surprise when I went to
fix 
an ePub with Sigil.
I clicked
open in the book browser, that showed epub as my only format.
Surprise: there was the same book in PRC in the folder (many of my Baen books were converted from PRC, so PRC would not be an unusual format to see
).
The DB Integrity check reports no errors.
Am I correct, that the check only tests for "Inner (file name.type) Joins", when checking for files present?
I have zero Python-Fu, so writing a tool to test for "un-expected files" report, is not within my skill set. Using Eyeball Mk I method, is (mostly) out of the question with 1100 books