My dealer is very good about parts exchange. They'll take back any parts that are not "shelf queens" and give full credit towards other parts. So, yes, I had a spare filter for the canister being replaced and they gave me full credit for it.The old filter elements do not supercede to the new part numbers. The new part numbers are also a few dollars more expensive each.
I'm surprised there isn't more mention of this in regards to the kit. It's a real bummer for folks who keep some spare filters on hand and then want to do this upgrade.
It never hurts to ask.