See
here.
You have to delete both .bin and .dat files (warning, the .dat file hold the current page, so either back the file up or write the page down somewhere). Then browse the folders with the Cybook, to have the .bin files re-created, and then you can copy the .dat files back.
I guess afterwards "sort by title" would work, but I don't really know, because my titles and filenames are the same, so it could be that my books are actually sorted by filename
