Just when I thought it was safe to return to the forums, you're about to annex Siena! No, NO,
NO!
Seriously, your corrupted saves sound like a very nasty problem. And it is really weird that it only happens if you use the CB and declare war. I presume that in the war you take Pfalz and force-vassalize Siena?
Have you tried saving the game immediately after the DOW, no other action? And what happens if you try to load the save?
I have zero experience, unfortunately, diagnosing save game problems. From casual reading in the forum I have the impression that common sources of these problems are hanging alliances or other relations involving a country that got annexed. But how you would find such a thing, if in fact that is the problem, I have no idea.
Does the EEP have anything unusual involving Siena and/or Provence that would lead to some sort of clash in the save file?
This sounds like a LOT of work, but is it possible to compare the formats of two saves -- one before the DOW, presumably OK, and one after, presumably corrupt -- and see if there is some kind of syntax error in the latter?
In some games I get a delicate period of a few years during which the game is highly crash prone. But if I can get through that period, the game is OK. And I've never seen a save game fail to load.
I truly hope you can resolve the problem, even if it means Siena has to live a little longer.

Goodness, if Siena causes your game that much trouble, think how bad it would be if you tried to annex France!
Back to the AAR, I particularly enjoyed the conversation between the Scotsman from Stadacone and the mayor of neighboring Bas St. Laurent. Nice touch on your part to keep the Scots involved!

And you had first cousins marrying (twice, no less). Was that really allowed back then?
Edit: I was writing this as you posted #256. So the DOW doesn't make any difference in the corruption after all. Could there be some event which is timed to June 1644 that is causing the trouble?