If I understand correctly, there's no way around this. Each game sucks up it's "starting context" into the save file and thereafter pays no attention to other files.
That is mostly correct, as it "sucks up" - nice term - the XML, which is where all the game data is, into the save files.
The one exception is bugfixes in the main game .exe itself, which is where most or all of the compiled programming code is. When they fix a bug that is completely contained there, the fix will apply to existing save games. But most bugs are either entirely in the XML, or in the .exe but with their fixes also requiring XML tweaks (or vice versa).
I play pretty epic games so just starting over is not an option for me since I was about 6 hours into this game before the error popped up and I'm not spending 6 hours to run into another game-ending bug.
Unfortunately, this is the problem you will run into when you don't wait a little first after new versions are posted. It does appear from the forum here that, as of the Friday morning silent update, there are now no remaining critical bugs in 2.5.