For whatever reason, I had some problems getting the updated version to launch through the itch.io app. I don't know if everyone will have this problem, but if you get a message saying the game won't launch, click the "Show local files" button in the app, open the "EmpyreanFrontier" folder, and run EmpyreanFrontier or setup.exe to install the game. (you might need to uninstall first) After this, you should be able to launch it through the app.
This is the first time I've done a significant update with itch.io's Butler tool so that might be the source of the problem (the previous update was the first time I used it so it uploaded the whole thing.) It's supposed to make it easier to download patches or something, but I might have to go back to uploading the whole .zip file for each update because that seemed to work pretty well.