Only if you have a problem with the MAF sensor getting contaminated with oil from the K&N filter. They probably made a note of the K&N filter in case you bring it in with problems and changed back to a paper filter, so they can blame it on the K&N.
Legally, if the oil from the K&N filter contaminates the MAF sensor, Ford is not required to make the repairs under warranty since the aftermarket K&N filter did cause the problem. The tricky part is if they claim that the K&N filter caused some other problem not associated with the MAF or intake air like the ERG valve or DPFE sensor.
The Magnuson-Moss warranty act states that the dealer cannot deny warranty service or void your warranty based only on the existence of an aftermarket part. They must confirm that the part was the direct cause of the problem.
According to the Magnuson-Moss warranty act, even if the dealer finds that the aftermarket part caused the problem they cannot deny your warranty claim. They are supposed to fix your vehicle under the warranty, and go to the manufacturer of the aftermarket part for reimbursement for their work. I think we all know that it will be a cold day in hell when Ford goes after another corporation when they can easily stick the customer with the bill.
...Rich