Your KoboReader.sqlite seems to be updating on its own, as others have suspected. Back it up, together with the other files. This may or may not be an interesting experiment should you decide to delete it to see what influence it has on what appears in the collection list. Caveat emptor, but wait until someone else gives you an "all clear", or a warning like, "watch out, you'll brick the reader".
What kind of message do you get if you attempt to open a book that is not physically on the flash card, but in the collections list? Personally, I have never set up anything in My Collections, and just sideload author-specific books from my PC.
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