My hunch is that the Airtran partnership will come to an end soon.

Both Airtran and Frontier still have verbiage on their web site indicating the partnership is valid.

http://www.airtran.com/faq/q/can_i_e..._frontier.aspx

On the other hand, I did not see a place to enter an EarlyReturns number when making an Airtran booking.

I would say Frontier should credit you in absence of any announcement otherwise.

To be safe, I would grab screen shots of Airtran's site when making a booking.