You can manually reset your clock - varies by country/time zone whether you can do it through the menu or have to resort to USB networking to a PC - do a search here for something like "reset clock" or "wrong time". Your problem is that after a software update the internal clock resets to an early default time - making your most recently opened books now the oldest, pushing them to the end of the list.
One suggestion - as you now have collections - make a folder "Now Reading" and put the books in it you're currently reading.
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