I believe the "bug" comes from the scripted modifier in the SetCapital command of the event. This will affect Naples, Rhine Confederacy, Warsaw and Westphalia.
So I have redone all those events where this appears to make sure the change does not apply (e.g. Warsaw is basically 25, but the modifier was 5, hence the issue, I reduced it to 1). Place them in the Events folder and replace the old ones with those.
Now, unfortunately, the only way to rescind the issue is to re-run the turn before the Grand Duchy was created, with the new event files.
If not possible or too late, the only way will be, in case Warsaw falls, to script a forced NM change of +100/-100 to both sides.