Gloopy, I don't think you are using the concept of "affirmative defense" properly (To quote Inigo Montoya in The Princess Bride, " You keep using that word. I do not think it means what you think it means."). When one asserts an affirmative defense, one is saying, "Yup, I did it but here is my justifiable excuse [the statute of limitations has run; I was insane; it was in self-defense; adverse possession; statute of frauds, etc]. The burden of proving an affirmative defense actually falls on the party asserting it...and, if you can't prove it, it ain't an affirmative defense....or at least not a very good one. 😊

However, I believe you are referencing the SC audit and not the actual failure to fly a SC assignment by the 4 pilots referenced in the Chairman's Letter.
I think most pilots would agree that the 4 brought this scruitiny on themselves when they were unable to cover a rotation assigned to them while they were on SC. While that was the triggering event for their audit, as I understand it from the Chairman's Letter, these were not "one off" events.

The real issue is whether the company's SC audit is/was able to establish a pattern of prior conduct (with any degree of reasonable certainty) that justifies the termination of those 4. Once the company presents its evidence, it then becomes incumbent on the pilot and his/her DALPA rep to undercut the strength of that evidence (which is not employing an affirmative defense). What we don't know here on this web board is how strong was the company's evidence establishing a pattern of conduct from the audit? Did the pilot(s) at issue have SC from, say, 08:00-20:00 yet KCM shows them entering another terminal at 14:15 and CASS shows them having activated a jumpseat listing out of their SC domicile on the 15:00 flight to their home of record and at 19:15 there is a Facebook post of them at their kid's baseball game several states away?
Going more to your point (I believe), the harder issue for the company is establishing the pilots were not in position for a SC period in which they weren't used. However, because those 4 were terminated and not merely disciplined, I suspect that any "retroactive digital footprint" presented to them was probably pretty clear and convincing. Further, we don't know what kind of admissions any of them made in their statements to the company.

As Chairman Bartells said in his letter, there is no question these pilots are entitled to ALPA representation but if your client is blatantly guilty and has demonstrated a pattern of guilty conduct in the past, the ALPA representative may have his/her hands tied by the facts and circumstances and, at that point, the rep is merely there to ensure the pilot's right to due process is satisfied and fighting for the least amount of discipline possible. As "they" say, when the facts are against you, argue the law. When the law is against you, argue the facts. When both the facts and the law are against you, fight like hell for the best plea bargain you can get. 😁