There are wrap up provisions in the master agreement that Cytodyn would pay large sums of money if the relationship ended. I believe they range in the millions but I doubt that Cytodyn would make payment of that contingent to receiving data already paid for.
I doubt that Cytodyn would file that lawsuit without having paid all undisputed claims with Amarex although there may be some disputed claims. Unless Amarex can get a stay of the judges order then Amarex is out of luck.