I've had the same problem, I left HTTrack running for 2 days, aborted
downloading to resume later, and when I resumed it deleted most of the
previously downloaded content.

I ended up having to mirror the whole thing again, and I made all downloaded
files read-only just to avoid deletion. The site did not went down in the
process.

Even if the deletion is a feature rather than a bug, please make sure the
feature is disabled by default, and please give an extra warning before
deleting anything.