I've been playing around with the sync feature the last few days, and I've noticed a few glitches as well.
One was that not all the documents that I added a date to in Scrivener seem to have been synced to Aeon, although that may be a user error - I told Aeon to skip a lot of them when I didn't have dates for the documents on the first sync, then added dates a few days later, when I had added a whole pile more new documents. I'm pretty sure I chose "skip" and not "ignore" on the ones it didn't transfer, but I could be wrong. It was a whole week or so ago, and that's a long time to remember which button you pressed.
Another was that some documents which didn't have dates in Scrivener and which I don't recall seeing in the sync list at all (otherwise I would have told Aeon to skip them for now, until I figure out their dates) suddenly gained dates in scrivener corresponding to the start date of the timeline.
Third, each time (all two times now) that I've synced, my process has been as follows:
1) put dates in the date field in scrivener
2) close the document in scrivener when I'm ready to sync
3) sync from Aeon
4) add entity participation, maybe adjust some dates from looking at the timeline
5) sync from Aeon again
In step 5, most of the changes I made within Aeon show up as changes needing to transfer to Scrivener, but both times I went through this process, there was at least one document that had a bi-directional update - even though the Scriv file had not been opened since the previous sync (in step 3).
Otherwise, this is a very promising feature, and it does seem to have picked up most of the documents and saved me a lot of typing.