The understanding was that if he lost here, he would probably lose on appeal also. This is why NY court was huge. That's why some people expected that the NY court would rule in favor of NFL, this is why:
Again, judge is known for going by precedent (Brady) and letter of CBA law. NFLPA agreed to the deal to give Goddell broad powers. In other words, "it's in the CBA so y'all fucked yourselves"