> You HTTrack a site and it's all OK, and then later some
> files disappear?  Well HTTrack can't magically delete
> files unless you run the program again, so there must be
> some other process on your machine doing something...

Err, except if the site has some 404 errors. 404 stands for "Not found" (=
"Does not exists anymore"), and in such cases httrack attempt to "match" the
same remote structure, to "apply" remote changes on the local filesystem.

So, yes, httrack can delete a part of the local site if you get 404 errors.
There's a protection that prevent httrack from deleting *everything* if the
starting page is in error (temporary connection problem), but a partial delete
is possible.