Just in case this is helpful, I noticed HTTrack was downloading what were
supossed to be ".zip" files as "randomfilename.html".

For this I didn't do much tweeking, I just went inside the folder in Command
prompt and ran the following command to bulk change the file extension of all
the files:

C:/foldername/ren *.html *.zip

That changed all the .html files into .zip files and once extracted they were
all there.