Head unit blinking, took to dealership.

I have a 2014 TRD offroad and the head unit seems to blink occasionally for no specific reason. The audio doesn't cut out, the screen just blinks black for a fraction of a second. I took my truck in today for its 20k mile maintenance/oil change and mentioned it. They said they would reflash the unit and that it couldn't be a loose wire because they're sealed units. I got it back this afternoon and they said they fixed it and that if it blinked again i needed to have video evidence to show them because they would have to change the entire unit.

So I got in my truck to drive home and two things happened: 1. my phone synced directly to the head unit and 2. I'm pretty sure it's still blinking but it only happened one time on the drive home.

If they had reprogrammed the head unit wouldn't it no longer recognize my phone?