I believe you cannot instruct AT3 in which direction to sync. If a change is made in AT3, it will sync that change to Scrivener, and vice versa. If a change was made in AT3 that conflicts with a change in Scrivener, it will not perform the sync but will instead alert you to conform AT3 and Scrivener to the same value.
As I mentioned in the parallel discussion, if it were me, I would perform the initial sync, make the changes necessary in both AT3 and Scrivener to bring them into conformity, then sync again. If this is what you actually did, yet got the results you reported, I’d try conforming them one more time. If that still didn’t work, I’d ask for help from support.