I have a number of questions in my list from math.se If I click the red X on one, it is deleted from the list. I deleted quite a number, closed the list, reopened it, and verified that they were gone.
Rewritten from near-scratch, StackStalker is a chrome extension that will monitor any question on any Stack Exchange site and let you know when something has updated. Don't sit there and mash your F5 ...