Then they should have mentioned that in their court filings!

The reason that the tariffs were collected while there was doubts as to their legality is that the US Government promised, in court filings (courts literally marked this as estoppel in a ruling: they are unable to change their mind on it, locked in argument) that they could repay this easily, and so courts allowed them to collect it while they figured out the legality. When they promised this, if it did require software changes, they should have done that then, or else they were lying to courts.

This is why the judges are not giving them any slack here. They promised to courts that this could be done easily, in such a way that they can't change their mind now. This is all very basic tenets of law that even non-lawyers can understand.