If we are sending out letters for the holidays that a customer can skip a payment for a fee and one of those customers is in active duty and has exercised his right under SCRA how would this be done?

State laws can vary on how you calculate the fee. In Texas, as an example, it is the interest that would have accrued on the loan. So the math is easy, principal x 6% x time.

The Bank I am auditing simply charges a $40 fee to skip a payment for their holiday loan extension program. Interest at 6% continues to accrue as always so effectively, if the $40 is considered "interest" they are charged more than 6% correct? They are charged 6% interest plus $40. So when someone has exercised their option under SCRA, they can elect to participate in optional promotions for free?

I agree it would be interest and usurious.