Check out
this thread for a sort-of solution.
Sony really should have implemented folder-based file management and not this idiotic database system which tries to rebuild the DB on every disconnect. Please don't anyone tell me that "50-1000 books are enough on your reader", that is your opinion, I do not share it. What is the point of supporting SDHC and 8 GB MS if you can't use it fully? /rant mode off
Anyway, as a workaround I've switched to using a couple of old SD/MS cards I had lying around and loading each with a set of books.