I think you are right there is something to be fixed there. 
At this stage, you would have had a way to regain the lost 
data quickly : erasing the new cache, and renaming the old 
one which should have been still intact, and then restart 
and choosing : "continue interrupted download" would have 
restored the whole thing to its previous state. 
I made the same mistake, and fixed it like that. But if 
before doing that you attempted a new download, then the old 
cache is lost for ever. 

The question is : when you cancel a download, in some cases 
HTTrack warns that the new cache is incomplete and proposes 
to restore the old, but not always. 

I really think something is to be done there. The present 
behaviour is a little "dangerous" as you have experienced.