I was also having this problem with file extensions being renamed (wrongly),
which screws up too many saved files AND links, making it hard to fix, and
after looking around, someone here said that all 3.4x releases have this bug?
(I can't and don't have the time to verify) and suggested a much older
version, 3.32 (in the downloads page now only 3.33 is available). 

I searched for alternatives and found WebCopy (by Cyotek) which do the job as
I expect it to (except "Make index file" feature which seems to be buggy atm).
But once configured everything works fine: for example ZIP stays uppercase
ZIP, and lowercase stays lowercase too. Also .htm doesn't get changed to .html
-- ALL extensions including binary files and even files without extension are
downloaded AS IS. Relative URIs in saved htmls are also fixed at the end of
the download process. Just spend some time reading the docs to set it up.

I wish HTTrack would get fixed & updated though, I have used it in the past
many years ago and it was enough for the job back then.