I had a similar issue when converting from Aeon v2 to v3. I settled on dleting old timeline and sync’ed a fresh v3 aeon from then current Scrivner manuscript. But then I ordered aeon manuscript to try and reflect the non-time sequential order of the original manuscript. Aeon foced these changes into Scrivner. I ended of refreshing to a prior backup of my Scrivner manuscript. Now I do not sync at all and Aeon only gets used for small scene tracking.
So how do I get that wonderful choice of which takes precidence shown above in that sync window. I do not see that choice… is it because there are too many changes between syncs? Should I try again from scratch and sync every edit session? Is it that I’m sync’ing a full reorder in manuscript mode when I do the manuscript order in Scrivner. Should I just not use manuscript mode at all?