Theoretical possibility of transponder chip cloning?

Here is how to reset the system or replace the ignition keys:

NOTE
This procedure is used when a customer needs keys programmed into the system and does not have two programmed ignition keys available. This procedure is also useful when programmed ignition key(s) have been lost and/or the ignition switch assembly has been replaced, and it is desired to erase key(s) from the passive anti-theft system (PATS) memory.
This procedure will erase all programmed ignition keys from the vehicle memory and the vehicle will not start until two keys have been reprogrammed to the vehicle.
Two PATS encoded keys with the correct mechanical cut must be available to carry out this procedure. One or both of them may be the customer's original keys.
If additional keys are to be programmed, refer to the procedure in this section: Key Programming - Using Two Programmed Keys. See: Antitheft and Alarm Systems > Procedures > Using Two Programmed Keys
If the remaining keys are with the customer and are not available with the vehicle, then instruct the customer to refer to the Owner's Manual under the Programming Spare (SecuriLock in North America, Safeguard in U.K. Or PATS for all other markets) Keys Procedure, for instructions on programming the remaining keys.

1. Turn the ignition switch from the Off Position to the RUN position.
2. Enter NGS/SBDS using the Ford Service Function (FSF) card. Select PCM from the menu. Follow the Security Access to obtain security access.
3. From the NGS/SBDS menu Select: IGNITION KEY CODE ERASE.
4. Turn the ignition switch to the OFF position and disconnect the NGS/SBDS.
5. Insert the first encoded key into the ignition lock cylinder and turn the ignition switch to the RUN position for three seconds.
6. Remove the first encoded key from the ignition lock cylinder.
7. Insent the second encoded key into the ignition lock cylinder and turn the ignition switch to the RUN position for three seconds.
8. Remove the second encoded key from the ignition lock cylinder.
9. The vehicle should now start with both ignition keys.

Please let us know if you need anything else to get the problem fixed.