[SquareWheels]

Thanks again for your reply, I really appreciate your help!! I may have been unclear on something -- Calibre is not actually showing books that I've deleted, it's simply giving me a higher number of books than I actually have on the device (you know the black text in the left corner of screen after Calibre reads the device that gives the number of books on the device and the number of books which are selected, if any), and I can't figure out where the higher total number of books is coming from.

I was guessing that it was coming from books I deleted just because I know of at least one deleted book that still shows up in searches on the Kindle as well as showing up in the green search bar in Calibre, but you cleared up my misconception about the green search bar.

I don't use any Calibre related or book collection related apps, just the full Calibre program on my computer without any additional plug-ins or anything. I have the ES File Explorer and the Evernote app on the Kindle, and that is all. The Kindle isn't rooted or modified in any way unless you count having Flash installed as a modification.

I now think the problem must be with the completely weird file structure within the Kindle, which is somehow hiding book files and not letting me get to them to try to delete them once and for all.

Edited to add: Calibre does add new notes from Evernote as books but I can always find those and delete them so that is not the cause of the higher number either.