It will be good to know what your Elite told you to do, that way we can tell you what you need to do that your Elite didn't tell you.

first your pcm requires flashing, not possible with your maxisys ,will need to buy an online sub from ford to flash this pcm in order to rewrite the vin number. a passthru and a pc is required as well, no android.

then  go back to pats and click on  parameter reset, if asked which module was replaced then choose pcm. 2 keys are required to complete the programming. good luck.

  did you do parameter reset? do that instead of erase and reprogram keys .was the option ( parameter reset) available for your vehicle?

is the security light on steady or flashing

  yes that is true, autel has let me down more times than I want to remember but also keep in mind one of the keys could be defective, even if it worked before, happened to me so many times, specially with aftermarket keys. read the data to see how many keys are actually programmed. usually when the light stays on steady it means its waiting for the second key, otherwise it will be flashing. when the tool says successful that only means that security access was granted and the relearn has started successfully but not that the keys were programmed. if you have access to the ids then give it a try otherwise get a third key and give that a try as well, do a parameter reset again and try all 3 keys, 2 of them will take. good luck.

  yes I know, but keep in mind also that the 2 available working  keys could have been previously cloned , which in reality there is only one. ford and mazda needs 2 keys to program and start the vehicle, once that is accomplished you can clone all you want and you could start the vehicle with 2 identical keys and not know they are actually the same key. now in the event that all keys are erased  or pcm is replaced etc ,and you need to program again ,they can not be cloned keys. maybe this is not the case here and its just a tool's software bug but keep it in mind for future reference.