I don't use it that way, but I believe the
Reading List plugin's 'Replace device with list, add/overwrite all' list sync mode may already do what you want.
SmartEject can be configured to prompt you to do a RL sync you when there's a Reading List to sync, and show you when there's stuff on the device not in your library. But I'm not interested in adding the 'delete' step to SmartEject itself.