Missing eraser tool in Markup toolbar
I previously had a problem where for some reason my iBooks markup eraser tool was replaced by another pencil after the app crashed while using the markup tools.
Thankfully, I found a solution that didn't need me to restore my iPad.
Solution: By deleting the iBooks app and downloading it again all the app settings will be restored, including the markup tool, and in this case, restoring your eraser where it was before!
iPad, iPadOS 15