Need help with tuning

I don?t know if it?s a noob mistake. But I followed the directions to the ?t? up to this point.
I?m tuning a 2014 charger rt with long tubes, catless Mid?s, 3? exhaust into flowmaster outlaws, ported intake, cai, 180 stat
I have a open ticket and have been back and forth with tech for a couple days now to no eval.
Here?s the problem I having. Mind you this is the 1st time any tuner has been hooked Up to this car. The vcm captured the tune and I was able to see the calibration. Before I went any further with tuning. I wanted to be sure the stock tune flashed back into the pcm ok. Well, it didn?t work out how I wanted it to. It started to write the tune back into the car when I was hit with a prompt ?one time software update to your pcm and you?ll never have to do it again? etc.
I clicked ok and after a min another prompt saying ?turn off ignition wait 10 sec, turn back on and click ok? I did that and it said init failed?
After which the uconnect is now wanting a anti theft code and the evic says depress clutch?
I?ve disconnected battery for 1/2 hour to 12 hours hoping the anti theft would go AWAY!
I?m at a loss here and I?m not sure exactly what the hptuners tech is thinking. He?s been very prompt with getting back to me and thrown some ideas but none of them have stuck.
So, I figured I?d post here to see if anyone has route I can take or has been in this situation themselves before.
Correct me if I?m wrong. But I?m thinking the anti theft has locked the ecu from being tampered with and until I get the code it wont take a tune? Or for whatever reason the pcm