For people having save file issues:
There was an update a couple months ago that absolutely did brick saves if you haven't played in a while. It was avoidable, but I wouldn't be surprised if you went several versions between without updating that you're just SoL.
However, something else that I notice as the game is getting bigger. The main menu takes forever to properly load. I'll go to load my save and it will appear that there aren't any there, but it's because stuff is still loading. I think it's primarily because of the gallery that they added for CGs. If you open that first, you'll notice that they take time to load.
So TLDR: If it appears that your saves are gone, open the gallery and wait for the CG to load first. Then check to see if the saves are still gone. They may just be "loading" to appear in the actual menu.