I removed Principia a couple of times during the game.

That seems to be the issue, this desynchronizes the state of Principia with that of the game. See also this post on the fora; your crash is similar to hypervelocity's.

Yes it was. Thank you!
However, please take it as a feature request to have automatic fixing of such borked savegames.

I don't see us automatically fixing borked saves. If at all possible, it would be a massive amount of work. We'd rather focus on improving the mod in meaningful ways.

Sorry, I was not clear. What I mean is to have the work I did, namely removal of that particular section of the save game data, done automatically.