Very odd. I’m guessing a guitar tech (luthier?) can resolve it. My stepdad had a 12-string that had warped where the bridge was: if you looked across the top of the guitar you could see over the years the tension in the strings had pulled the wood up and dragged the bridge forward! When I took it to the guy under Hank’s he managed to somehow restore the intonation and everything and it played great again.
That’s why I can only assume it’s something like this that’s suddenly gone and changed the scale length just enough? 
Hope it gets fixed.
