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I've set the Stages and Skills for my teams in Portfolio but I cannot seem to make exclusions for specific Epics when estimating on the Scope view.
Since skill based estimations are all cumulative, I cannot seem to override the whole estimation with just one skill.
See below screenshot, a particular Epic can require only Backend work:
The Epic is going to have a roll up of all the child issues contained in that epic, so you are going to want to look at the estimates at the story level to influence that roll up.
Looking at this screenshot:
Expanding the skills looking at ASDF-2 the estimate is at the story directly but the other two are estimated at the Skill, When estimated at teh story level it distributes the points out across all the skills, then rolls up to the epic.
Looking at the next Screenshot:
I set all 3 stories estimates at the Same skill now so now only that skill rolls up to the epic.