While trying to figure out the SmartEject issue, this happened:
1. I searched #readorder:true to bring up all the books on the reading list.
2. I used Ctrl+M to toggle mark on all of them.
3. I went to Reading List > Clear list.
This removed all my marks, which I was using just so I knew which books to re-add to the list.
Was that supposed to happen?
EDIT: I wasn't able to replicate it a second time (this time I set the #lastread date to next year so I could find the books again). Gremlins again.