Started on Wine, Got Rather Far, Now On Native Linux Have to Start Over?

[Gigakoops]

I mean, I guess I don't mind starting over, but I did unlock quite a few endings when running the game on Wine. I've even uninstalled and reinstalled onto different instances of Wine, and my save data carried over. However, when I went to the main menu on the Linux port, I noticed that all the endings I unlocked are gone. Has anyone else experienced this? Should I wait for a patch before playing, or just start over?