At some point as I was working in my file, it became the auto-recovery version. I was saving normally and when I exited the program the auto-recovery file was still sitting on my desktop. When I re-opened the original file, the auto-recovery was deleted automatically, but I realized none of the work I had been saving existed in the original.
The auto-recovery wasn't sent to the trash, but wiped, and I need to recover it or basically lose hours of work.