My somewhat dodgy system occasionally screws up while GC2 is auto-saving, and apparently GC2 deletes the old auto-save before creating the new one. As a result, there's no auto-saved game at all after one of these crashes.
I suggest keeping the old autosave around while the new one is being created. Maybe keep a couple around in case one turns out corrupt.
The work-around is just to save often, but I forget to save when I'm getting caught up in galactic domination