You could:
1. have the dev that wanted to do this delete the images folder after publishing, then upload to PixRiot as normal. Only overwrite the files that exist. It would be the responsibility of the dev to re-publish the project to create and copy the image files again.
2. leverage the "upload online" dialog to post directly to PixRiot. You could save the PixRiot login information to authenticate, then use a master FTP account to access it behind the scenes. Leaving the "skip images" checkbox checked would then apply and only upload non-image files