I don't believe there is a "fix". It's inherent in the Sony operation. It scans the memory/cards for new material and reorganizes the internal library each time it is cold booted or something is added/removed.
I only have about 100 books on the reader at a time - probably more than I really need since I only read one at a time. I delete a book from the reader when I've read it. The rest of the books in my collection, both read and unread, I keep on my PC and manage/organize with Calibre.
I realize this usage is considered radical by some owners, but I just don't feel obligated or inclined to have my whole collection available on the reader at the same time. This works for me.
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