I believe synchronization is a function of spindle speed. Moving the start point back and forth in Z does not (should not) change the sync engagement, provided that you make the initial tool setting on a fully formed thread, not on an initial scratch pass.
I would run the full thread cycle, even on the reworks, until I was sure that the tool was safely retracting at the end of the thread. Wouldn't want to run into heavy cutting at a critical moment
