I would not expect the Ford service staff to clean them, just not replace the filter and then toss the K and N filter out.
K and N will, according to their web site "deal" with the dealer service department for you if there is a warranty question about using K and N air filters.
May be the best way to solve the problem is to put the paper Ford filter back in before you go to the dealer for service, then replace it after you leave.
But you may be charged for a air filter that you don't use.

Maybe Carbon M had the best idea, just service it yourself.