The court would not be negating that fact; rather, the court may rule that the Cert is not active for purposes of this particular case; or the court may rule that it can only be applied prospectively.
There is much case law that both sides will throw out to support their respective positions; one of the points I made previously was simply that I have been unable to find (and I presume SG is not aware of any either, otherwise they would have proferred it up) any case law that incorporates all of the unique situations that exist here, namely (1) Cert was due to "minor" clerical error, and (2) Cert was requested AFTER lawsuit was filed on said patents.
From the perspective of fair play, what is right, and what is just, this is slam dunk case. However, as we all know, what is fair, right, and just oftentimes do not sync up w/"the law". This is where the risk lies from an investment standpoint. Inflexible rigidness on some regs that seem to go against the spirit and intent of what the regs were designed to do; technicalities and loopholes that let offenders off the hook even though they are unrelated to the substance of the case; etc, etc, etc...
Judges do their best to issue rulings that are in line with THE LAW as they understand them to be -- not necessarily to "do the right thing"...