> were missing. I started to download them, and in the
> process all the pages I had recently downloaded were
> no longer where they used to be.
> 
> Where are they? I really can't wrap my mind around
> the idea that all the files would delete themselves

Did you do an action=update or did you override?Did the update complete?
Successfully?  The default is to delete obsolete files from a mirror at update
completion. If the site was down, then all the files in the mirror are
deleted.