CBS has done the right thing. When you call, make sure to have your Blu-ray set in-hand. They'll need proof of purchase info. You also won't have to mail in your flawed discs to get the replacements.

From the press release earlier today:

Dear Star Trek Fans, We have discovered an anomaly in the English 7.1 DTS Master Audio track in our Star Trek: The Next Generation Season 1 Blu-ray Box set.

There are some episodes that inadvertently had their front channel designations incorrectly mapped, resulting in an undesired playback experience when listening to them in a 7.1 or 5.1 Surround Sound environment.

We are quickly working to remedy the situation. Replacement discs (Disc 1, 3 and 4) will be made available free of charge.

Please email phe.stng@bydeluxe.com for details regarding the replacement program.
You may also call 1-877-DELUXE6 (877-335-8936) between 8am to 6pm Pacific, Monday-Friday. We strive to provide our fans the best Blu-ray experience possible and sincerely apologize for this inconvenience.