I understand the point you're making and agree that it looks like there may be a deal.

My concern is whether having, effectively, lost the claim on infringement of 445 and 108 as a result of the dismissal with prejudice, sets a precedent that diminishes the potential for success in pursuing infringement by other companies unrelated to Samsung.

This concern is prompted by the following explanation of what dismissal with predjudice means:

By contrast with prejudice means that a party's legal rights have in fact been determined and lost. To continue the same example, if instead the court had jurisdiction, but the plaintiff did not appear for the trial, the court would dismiss the case "with prejudice". That dismissal is a judgment against the plaintiff "on the merits" of the case, and extinguishes the claim that was being sued over. However, this does not prevent an appeal or a trial de novo if ordered by a higher court.