If a re flash is in order, it might have to be an aftermarket software and programmer. The factory scan tool used to flash the ECU's are VIN specific therefore, if the scan tool is installed on the vehicle, it will read the PCM VIN first and populate the available flashes for that specific build however, there is also a box on the menu that you can manually input a VIN and program it that way. The issue then will be the ECU part number. If the ECU is built with a SKREEM/ SKIM system and you program the ECU with a Non SKIM software it might not enable the ignition sense circuit within the PCM and not give you an ignition sense output( no start). By the time you get this figured out if it will work or not, I think your better off in getting a re manufactured or new PCM that's specific for your Jeep instead of a Rubicon model.