I tried hiding everything and calibre was able to read it just fine. I scanned a book and put it into calibre. Calibre seemed to take it. I unhid calibre's folder and the recently added book was there. So it appears that calibre can fuction just fine when its folder is hidden. Keeping it hidden will reinforce the black box concept; out of sight, out of mind. I also won't have to worry that if someone should get into my computer (not likely but I'm paranoid), they won't be able to get into that file and wipe me out (I have it backed up but restoring back ups is such a hurt in the donkey).
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