Hey Dave,
thanks for the reply. I had not deleted the autosave up until this problem had occured.
A solution I worked out is as follows:
1) rename the savegame folder (...\steamapps\common\Technobabylon\Saved Games)
2) start a new game (to recreate the savegame folder)
3) copy the most recent savegame (or the savegame you want to continue from) into the new folder
4) load that savegame
5) save in a new spot (agssave.001 will be created)
6) delete the old copied savegame
If you do not delete that savegame, the problem will reoccur. So again I think it does not have anything to do with the autosave.
Of course this does not solve the problem in itself but is a workaround. And I hope it helps future visitors that have the same issue.
At least I can now continue playing.

Did I say, how awesome this game is?

Best wishes,
basseur