One remote, though plausible, scenario is that the Rams/Chargers/Raiders move created some fault lines that have left Goodell fearful for his own future, and he needs to woo back some of the owners he may have alienated over the past couple of years, including Kraft.
I mean, at some point the sheer quantity of negative shit surrounding the league has to reach a tipping point where Goodell's head gets put on the block. It's been 2 straight years of nothing but shit sandwiches, from concussions, to spousal abuse, to AP smacking his kid around, to deflated footballs, to the military paying for pregame shows, to getting smacked down in court (again), to Johnny Manziel, to the league's #1 star, fresh off of a Super Bowl victory that the league surely hoped would serve as a reminder of everything "good" about the NFL, and a pushing of the reset button of sorts, getting dragged through the mud in a very public fashion.
Granted, lots of this isn't Goodell's fault, but the Jerry Joneses of the world do not give a fuck. Super Bowl ratings were down. Lots of owners were pissed about the LA move, and how it went down. Now they have the joyful prospect of the league's biggest offseason story being a public shaming at the hands of the court of appeals. Oh, and not to mention whatever else some scientist discovers about CTE, or what other young star decides to hang 'em up out of health concerns.
All that in mind, maybe some owners look back on the overzealous handling of Deflategate and say "You know, it sure would be nice if that had been wrapped up a year ago. What the hell was Roger thinking, again? Explain why he didn't just strip a 3rd rounder and be done with it?"
And, yes, the Brady case isn't *really* about Deflategate, but this is, what, the 3rd bite at the apple that Goodell has attempted in securing some arbitrarily large power to discipline players? If I'm an owner, I start to see this as a pride-driven, quixotic, quest that's doing more to embarrass the league than secure some sort of upper hand that benefits ownership. That goes double when you stop to consider the ostensible reason for securing the out-sized power for Goodell is to be allowed to punish players severely to make the league look good by showing how "seriously" they take issues like "integrity of the game" and spousal abuse.
The best case scenario for league, at this point, is a Pyrrhic victory.