The NFL's only case is the article 46 and nothing else matters. They're doing everything they can not to be dragged into a debate about the factual merits of the case, whether there was evidence, whether it was fair, whether Brady had proper notice of the penalties, they know they lose on all these points.
IMO, the NFL lost the chess match with Kessler/NFLPA. Kessler went after Pash in the appeal knowing the NFL would be reluctant to let him testify, and if they did, Kessler knew his testimony would be damning for the NFL once it went to court. There's also no way Pash could perjure himself, so if he ended up having to testify the NFL would be finished (in court). Kessler/NFLPA knew that the appeal was going to be a farce, attempting to convince Goodell of Brady's innocence was never going to happen, it was about making the NFL do things they would be uncomfortable doing. The NFL should have never linked Pash to the Wells report, Pash should have never edited it. The NFL could have gotten away with this witch hunt, but they didn't think enough moves ahead.