Welcome to the forum!
Moving the skimmer isn't too big a deal. However, you'd need to not only patch the wall were it was but also, patch or replace the liner.
An easier way of dealing with this would be to incorporate a lid in the new deck for skimmer access. Folks who have decks all the way around their AG pools might be able to post pics of what I'm talking about.
Good luck with the new deck!
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