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hmm, unfortunately I'm not sure why. do the two files in the 'persistent' folder look as if they have been created around the same time that you played this game? 

one suggestion I can make is to have a folder called "Ren'Py Data" in the root folder where the unzipped game folder is, and renpy should automatically save the save files there, but that won't bring back the saves you've lost.

Nah, neither one of those are yours. One is from Katawa Shoujo, and the other is from Nomnomnami, which I should probably purge since it's acting funny. I'll try putting a folder next to the game and see if that helps, thanks!

let me know if it still doesn't work! I haven't been able to recreate the issue on osx myself, but I'm trying to see what else could be the issue.