Yesterday I made sure all of the books in the "My Kindle Content" directory were indeed added into Calibre (they were), and then I deleted all of them. Restarted Kindle for PC and I had back only one copy of each book in the library, and covers were showing. Partial success.
But that annoying fake book about the $.99 charge my bank didn't like is forever there, so I decided to annoy Amazon with it this morning
. After over an hour and going through 2 reps, they decided to escalate it as a bug to the developers and they'd get back to me. But the last rep gave me $10 in my Amazon account for books! So it wasn't a total waste.
Steps taken to remove that fake book: I de-registered Kindle for PC as one of my devices, uninstalled it totally, reinstalled it, re-registered it (each step at least 3x) and still that fake book that won't download or open remains there. The rep had me delete the book the note was about from my Kindle account (which as I suspected did nothing about the fake note still there), and she had to then manually give the book back to me.
From now on I plan on deleting everything from that directory once I have it in Calibre. It seems that if I ever open a mobi book from anywhere else with K4PC, that the program automatically not only adds it to the library but also copies the book into the "My Kindle Content" directory, and there doesn't seem to be any setting to stop it from doing that. So that's probably where all the duplicates came from, if I had to check a problem on the conversion to epub, I'd open the mobi to check if it was present there (and it usually was). Open the book again later, and K4PC adds the same book yet again. Really horrible software.
But at least I get a free book out of it or more depending on cost.