They accept to pay X  for anticipated validity rather than risk treble damages and possible lengthy and expensive appeal process, but still have some concerns over validity so they agree to pay Y when re-exam results are final and favorable to PTSC/TPL. Meanwhile, they get to carry on business as usuall with a contingent license agreement!

Everyone who has signed a license agreement to date also knew the risk of having the patents invalidated in the re-exam.  They weren't interested in lawsuits because it was probably cheaper to just sign and go on with their business.  They know they won't be getting a refund if the patents are invalidated....maybe the Js realize there will be no refund so they would rather pay the big big bucks on contingency.

 It makes sense to me but what do I know LOL....