Update, for what it's worth.
Over summer, and after getting the place properly watertight the wood gradually straightened out. It's not perfect but getting there and all bay one of the sills are pretty much acceptable.
I think the problem was that the underside of the wood was more humid than the top side which could dry out.
Lessons are: don't expose wood to repeated large changes in temp and humidity over a prolonged period. If you do however, be patient, there's a chance that it will fix itself.
So glad I didn't panic and replace them.