One theory I heard (non-confirmed) is Kraft new he'd lose the suit because of that promise not to sue the league thing and got a promise from Goodell to make the appeal unacceptable to Brady and the NFLPA and he will help that suit.
Unconfirmed, and Kraft will have to be quiet in his helping Brady's suit, you know, attacks that hurt the NFL more than help it but he ca claim incompetence instead of underhandedness. Depending on how well he acts, this may never be confirmed. If Brady sues, wins, and we get the draft picks back, I will consider this a successful "Batman" gambit by Kraft. (Yeah, that is a big if.)
Definition of "Batman" Gambit for those curious. Oh, it has nothing to do with chess.