There's nothing written or "programmed" as you say. Disconnect and it's stock. zero trace anything was there other than physical seeing the unit(s) installed if still there.Does not Jeep have the ability to tell if an unauthorized program was used on the engine? I know GM scans before any work.
Luckily, we don't have any of those where I live.What kind of recall/warranty work are you having done? If it's anything under the hood around the engine wiring harnesses, a competent mechanic will see it and know what it is. Anything involving just the OBD port for software should be just fine when the Banks cable is unplugged and tucked up.