If I understand your question then here has been my experience with a similar result: If for instance you need to start re-recording at measure 12 (because of a mistake etc.) then set your digital recording to punch-in at measure 12, THEN, do a RWD back several measures to start from. That way everything is in sync by the time it gets to measure 12. Make sure all you set-up conditions are still in effect though.
Hope this is what you are concerned about.

Dick