Hey,
at the moment when we export projects, Webflow adds all .html endings again. Since we use a .htacces rewrite command, we have to remove all “.html” endings in href links again. Could you add a checkbox when exporting so you can do the export without .html endings?
I hope this is in the right place. 
Sincerely Pascal
I would suggest reviewing the wishlist and voting your preference. See Webflow Wishlist
Pathfinder on OS X or PowerRename (MS PowerTools) get the job done with no fuss. You could also script it.
Which hosting service are you using? I would recommend using Netlify as they have a feature to give your manually deployed website’s a pretty url. Works every time for me!
Hope this answers your question.