Brian Karis's time with Naughty Dog seemed rather short. While I couldn't find anything on when he did start with the company, his LinkedIn profile had him at Epic Games and wasn't even updated with his stint at Naughty Dog.
That said, Brian, a senior graphics programmer, is leaving Naughty Dog to go back to Epic Games. Even his Twitter said the quick turn around time was "quite strange".
It's normal for folks to come and go from companies, even if it is a huge one like Naughty Dog. Sometimes, even good companies aren't good fits and this seems to be the case for Brian.
Brian spent his first seven years with Human Head Studios and then transitioned to Epic Games.