So I just deleted my prefs.ini file to reset my game settings (changed something, couldn't tell what) and when I reloaded my last save the goody hut with +20 research taht I was just about to get is gone!  I know because I had loaded it twice before to test the settings and the hut was there.  With new settings, it's simply not there!  Same save! 

Is there some way to fix this?  Does the prefs.ini file control even the ingame settings for difficulty and resource density and stuff?

Thanks.