> all files had been purged. Is there any way of 
> recovering the original files that were downloaded in the 
> first run?
You can"t recover data files, but html files should still 
be in the cache (just remove hts-cache/new.* entries - 
httrack will use the previous ones)

HTTrack always attemps to "synchronize" the remote content -
 and if the site is partially gone, it will cause partial 
purge. If the site is gone, generally httrack will detect 
the error, and won't issue any purge. If the site was 
replaced by a "fake" error page (with status=200), the 
purge will be issued anyway.

You can disable this behaviour through "don't purge old 
files" (Set Options/..)