As of this evening, the Union Pacific licensing program page is unchanged from earlier this year, and it still lays claim to Alton and Southern and American Refrigerator Transit but not Chicago Great Western or Chicago St. Paul Minneapolis & Omaha, those CMO grain hoppers notwithstanding. That makes for amusing reading of the latest Atlas O offerings (.pdf). You could buy a Chicago Great Western SD-40 (not licensed) or a Clinchfield SD-40 (CSX licensed.)
It probably also dawned on Union Pacific (but clearly only after someone refused to cave over a lawsuit) that they were using high-priced attorneys to collect what must have been piddling amounts in license fees. I doubt if anyone did any serious analysis on how much blood they could squeeze out of the model train hobby turnip, while at the same time they were damaging their image among a group that should have been on their side.
(UPDATE: Further comment on the forums suggests that [Mike's Train House] turned the legal cost-benefit tables on Union Pacific. MTH's discovery requirements for Union Pacific documents were enormous -- for instance, they subpoenaed every company e-mail that mentioned "model railroads". Union Pacific, which presumably had begun to realize what small potatoes royalties on $10 or $100 model train items really were, must have come to see that there was no possible way they could make money on royalties if they had to pay lawyers to answer all those subpoenas! They chose the wrong patsy indeed.)
Is it any accident that the two railroad companies currently facing lawsuits from Amtrak over delaying the passenger trains are also the ones with these licensing programs?