Ahh, I think I might see what the original poster's issue might have been — you must be in the notebooks main panel in order to do this. If you have notebooks expanded in the sidebar for instance, right/option clicking the notebook in a stack (or dragging and dropping it out of the stack) will not help remove it. I almost always have my notebooks and stacks expanded in the sidebar so I bumped into this issue today too and found this forum. Hope this helps somebody!
How to remove a Notebook from a Stack
in Evernote for Mac Issues (Versions 7.14 and under)
Posted
Thank you!