Taking say 12" out of the leech will have a totally negligible impact on performance. Tell the local PHRF handicapper and I bet he/she wouldn't give any adjustment.
I don't see how this should impact the reef points, as the reefing
lines should tie around the boom so they can self-adjust as necessary.
Let the sailmaker figure out the proper dimensions for the new sail...getting it right is one of the reasons the local sailmaker charges big bucks...