Anytime you change something in your shot you will affect your gaps and you will have to spend some time with the bale to relearn them. Does not matter if it is your nock point, rest height, arrow length, point weight or length, shooting glove or tab, or arrow rest to name a few.
Since you changed the relationship of the arrow to your bow hand it does not matter if you move your nock height the exact same amount upward and have the exact same anchor. You have just slightly changed the tiller of the bow to your shot and your bow arm is going to be in a different spot in relation to your eye with the elevated rest. You may have to adjust the cant of the bow to get the arrow back under your eye properly as well with an elevated rest and that can also not only effect the gaps in gap shooting, it can also effect windage.
All in all though, there should not be THAT MUCH change in gaps.