Hmm... That IS a problem.
If only Sonar had a "master tuning" feature that changed all the plugins at once!
Other than that, I really don't know how to even save the edited tunings on a plugin!
I DO understand the need for it completely though. We record our music at 432Hz vs 440. I invested in a Peterson strobe tuner that would let us accurately tune everything.
What about recording the instrument first? Then add the rest later, one by one, so you wont have to worry about the instrument changing it's pitch?
Just an idea. Good luck!
Peace!