Did you ever export the bookmarks to some other location?

Have you checked to see if the file was not merely renamed and left in a dumping ground of "lost" files... like what Scandisk does with orphaned file blocks.

Not knowing how your disk recovery program works, I dunno what it does with the files it can't find, or finds but in broken state. (Ignore, overwrite, try to fix, or truncate and so on)