Simple. The Appeal is about the Commissioner's power under the CBA, not about the data. That is why they have a former Solicitor General as their Appellate Counsel and why I hope Steffen Johnson is the right guy to go toe-to-toe with him.
They want to make this a landmark case about the rights of management and are throwing the equivalent of a Hail Mary pass that they get two Second Circuit judges on the Panel who are sympathetic to that view, after the debacle they confronted after outsmarting themselves by rushing to get the original Case heard on their own turf and ending up with an old-line, Progressive Judge, put forth by Daniel Patrick Moynihan, who tossed them out on their butts.
The NFL is more or less saying, even if the data were a complete fabrication, we still had the right to do what we did. Berman found that they erred in process (notification, etc), but his comments on the "investigation" itself into the data were sarcastic and of the nature of an "aside." (Berman could open the whole can of worms again if it gets sent back to him on the matters he left un-considered in his ruling, as, some have argued, a "time bomb.")