K&N makes a stock replacement filter, the only way they would know you have it would be to take the cover off the box. It might be a happy medium in your situation.
Or try another dealer for warranty work. My Service Mgr loves my focus and the things ive done so far.
ZETEC Crew #26 SR #20 YELLOW BLAZE OWNERS GROUP#4
Moderator Pilot, 12 SE HB ╠╬╝, 2011 Ford Edge SEL AWD