Do you still have your downloaded folder for the last version of the game? It sounds like it somehow overwrote your save file with a fresh one before when you were in compatibility mode (though I'm not sure why it would do that), so just deleting the new .ini will only make the game create a new fresh one. If you can, you want to take the old .ini from the version of the game you played before and copy/paste it into the new folder to replace or overwrite the new .ini.
Unfortunately, if you don't have an old .ini, you might have to start over, but if the game is working properly you should at least be able to unlock the other modes again through playing.