I really don't know enough about the structure of the game to comment properly but I've had a similar experience but for different reasons. The game officially isn't out in my country so I pirated it to see what it's like. I flipping loved it and then found (to my delight) that impulse doesn't seem to care that it's not out in my country and let me buy a Digital Download copy (thanks Impulse!) 

So before I let Impulse do its thang I uninstalled my pirated copy. With the Digital Download copy freshly installed I fired up the game and found that it had deleted my favour points and my achievement but curiously not my alias nor save games! I'm still going by my old name in single player and I still have access to my tournament save games so I did a bit of sleuthing and found the following directory:

C:\Users\[My Name]\Documents\My Games\Gas Powered Games\Demigod

That's where all the saves, the profiles and the replays are storing themselves along with the game's preference log. So I presume that whatever it is that holds data about favour/achievements is somewhere in the actual install folder. So for me, uninstalling the game got rid of it along with the game's data. For you ... Well I'm not sure what's happened for you. You might want to do a bit of sleuthing yourself and see if you can find a file likely to hold favour/achievement information. Back it up!

Good luck!