All of my bookmarks disappeared today. Folders are still present but they are emptied. Backed up recently but no luck restoring - just empty folders.

Is this a bug in the program or can another explanation be provided?

They're not gone. You probably just switched to a non-Bible volume.

If you create bookmarks in a Bible (and/or a commentary) then switch to a dictionary or other type of book, the bookmarks don't display (because they're not applicable to the current volume.)

Switch back to a Bible and you'll see them.

Incidentally, you can create bookmarks in those other books as well, and they'll show up -- but only when you're in those specific books.