So I finally figured out what the heck was going on.
I changed the name of my mod in the project settings. Well the name I changed it to was "Timed Autosaves for D:OS 2".
Only problem is Steam apparently likes to rename the actual pak file as the logical name you give it in the project settings. The editor itself does not do this when uploading. Which would be fine if I hadn't used a character (:) that windows can't write as a filename.