Sonic03Cobra

ok so i have a 03 cobra and i just orderd some performance parts and got a predator programmer.. and i pulled the stock tune out and they wouldnt go back in.. i later found out it wouldnt put them back in cause it had a super chip.. does any one know if i pulled the advanced tunning out of the chip and put that on the programer as stock? casue im afraid that i took the performance tune off the chip and put it in the predator and then when i go to run a performance tune im gona have double the timeing and everything.. does any one know if this is possible? or what.. i think i need to put all stock in my car and have ford reflash it just to be safe.. any ideas.. thanks