And that flatly contradicts what the plaintiffs are asking the judge to do. Disavowels that the USPTO didn't act on, but want the judge to see and enforce.

The USPTO doesn't disavow anything. The moving party who is prosecuting the patent is the one on record for disavowal. TPL made statements during the prosecution of the patent. The T3 are attempting to use those statements during the prosecution of the MMP at the USPTO to persuade Judge Ware that TPL disavowed certain emobodiments of the invention during the reexamination/revalidation process.

Ron is correct. Judge Ware is not looking at what the USPTO did. He is looking at the prosecution history and determining if TPL disavowed any emobodiements of the invention.Validity and Infringement are different. Typically, the USPTO can only determine validity while the courts typically determine infringement.

Hopefully the above clears it up for you.