When you install the Trifecta tune the first thing you do is make a backup of the factory ECM files on your computer. Then you install the new tune, I can't remember sending a base tune to Trifecta. Trifecta would most likely have to create a base tune from a stock file they have.
I would contact BNR tell them you have a Trifecta tune on a used car you purchased and want to switch to a BNR. Tell them you bought the car used and have none of the equipment or files to switch back to stock. BNR might be more helpful since you are trying to switch over to a BNR tune. BNR does have the option of forcing a full flash, maybe you can force a full stock flash using BNR equipment?