Ok, so I did this:
1. Plugged in device.
2. Deleted every book from the device.
3. Removed the books from the reading list.
4. Used SmartEject. It didn't ask me to sync the list.
5. Re-added books to reading list.
6. Plugged in device again.
7. Synced reading list.
8. Used SmartEject. It asked me to sync the list.
I'll just uncheck reading list in the settings and use SmartEject for a handy big eject button I guess