I've been downloading multiple webpages (single pages including all of their
cross-domain resources) to a single folder.  

Each time I download a page, an index.html and several other files are
created.  I rename the index.html to the name of the webpage, and generally
delete the other files (though not 100% of the time). Should this cause any
problems? Especially problems that would involve web resource folders being
deleted?
This process was working fine, until rather suddenly I noticed that the
majority of the pages I've downloaded have had their resources deleted
(specifically the relevant resources.. the main website name folder remains,
but sub-folders that contained the .html files have been deleted. Oddly not
all html resources are deleted, just the majority of them...  I am at a loss,
I have never seen a drive fail in this manner before, and my paranoia makes me
suspect I was hacked/infected...

I'm hoping you'll be able to tell me httrack is the culprit, even though that
seems somewhat unlikely.