I originally synced Scrivner manuscript to Aeon then I rearranged aeon in the manuscript/chapters to get it to properly reflect chaper order vs the timeline order which were different. Then I continued working in Scrivner. When I opened Aeon and selected Sync to Scrivner, all my changes in Scrivner were lost as it overrote the Scrivner manuscript with the earlier version plus lots of wierd organizations.
How can I make Scrivner source of updates in sync?
How can I work in either and specify which is the source for a specific sync?
When you performed the first sync, the Narrative and Outline views of AT3, but not the Timeline, Spreadsheet, or Subway views*, should have conformed to the Scrivener manuscript structure you’re using (chapters, in your case). From that point, any change you make in AT3 will, upon syncing, update Scrivener, and vice versa.
I would again try to reorganize things in either Scrivener or AT3, then sync again. My guess is things will work as expected, but if not, open a ticket with support. They are always willing to straighten out this sort of thing if you’ll provide the files.
*Note: In the forthcoming vers. 3.5, this behavior may change.
Update: I see this is also being discussed in another thread.