Not sure what you mean. When you re-sync, the meta-data you've specified (if you've specified start and end dates, for example) will be transferred to Scrivener, but if you're talking about re-arranging the order of files and folders in Scrivener, no , it won't do that - you'll have to do it manually, although it can be done within Aeon Timeline.
Thanks Craig. Yes I wanted to rearrange them simultaneously from Aeon towards Scriener. Pity it doesn’t work.