> when i delete one of the subdirs from my list and want to 
> update my local copy all files within that removed subdir 
> are deleted w/o a warning.

Yes - httrack always tries its best to synchronize the 
remote state and local state. This also means that is many 
files were deleted remotely - or if you removed starting 
URLs, like in this case-, many files will be deleted 
locally.

You can use the "do not remove old files" option to prevent 
this behavious from occuring.