P0454 CEL came back on

Three months ago I got a P0454 "EVAP Emission System Pressure/Sensor Switch Intermittent" CEL out of nowhere on my '15 Mustang GT. I cleared it and checked things out and found nothing out of the ordinary. Fast forward to 3 months later and I went to check my ngauge and it came on again today. I'm lost on what to check for. I searched online and there is a Ford TSB for that same code and it talks about a PCM to the latest calibration. I'm also tuned and run a Paxton Supercharger. Question is... if I take it to the dealer and flash it back to stock and they then flash the PCM to the most current calibration according to the TSB, can I flash my custom tune after that or will I run into issues? Lastly, is my tuner able to disable the P0454 CEL in my tune? Thanks

yes, he is able to shut off that code in the tune

Thank you very much.