So I used my Akeeba BAckup file and kickstart to "restore" a version of the site in a sub-folder, we'll call that Site B.
So to even get kickstart working I had to add the sub-folder for Site B as an exception in the "Allow direct access, including .php files, to these directories" area of the .htaccess tool. Okay no big deal.
So the restore goes fine and Site B is supposedly up and running. Backend of Site B works fine and the front page of Site B is fine, but if I try to use any link on Site B, such as clicking on an article, I get a 404 error.
Can't seem to figure out why and not sure if the problem is on the Admin Tools for Site A or Site B. I want to get Site B fully functional before I start playing around with upgrade stuff. I could just turn off Admin Tools on both but I'd prefer to have both functional in case of any conflicts.