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If you have the option checked, SmartEject asks Reading List if there are any lists that aren't sync'ed and offers to sync them. If you say yes, it tells RL to sync, same as if you had used RL's 'Sync Now' option.
I have, on occasion, seen a list become confused and think it needs to sync when it doesn't. For example, if a book is added to to a sync-to-device list while the device is attached (or doesn't auto-sync when attached) and then the book is deleted. Because RL is not notified when books are deleted, it still thinks that the list needs to be sync'ed even though it really doesn't.
However, in that case, you just let it sync (which takes no time), hit smart eject again and now it passes the sync check and ejects.
OTOH, I use 'Add/Overwrite all items' with 'Clear list on Sync' checked and you use 'Add new only' with 'Clear list on Sync' unchecked. I don't know how that may effect you differently off hand.
But I suspect the answer is: Sync the lists and hit Smart Eject again.
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