I discussed this with Rav Dovid Morgenstern (one of the most prominent poskim today, a talmid of Rav Eliyashiv zatza"l) by phone, and below is a partial transcript of his reply:
It's complicated. Mitzad echad, it's only one witness, so he doesn't have any neemanus al pi din. And he also doesn't know for sure how far it went. But what we'd like to do is to cause it to stop before anybody gets in trouble. Because we'd like to preserve both marriages.
Now, if we know for sure she had relations, then we have a different problem, because the woman is forbidden to her husband. We had a few cases like this with Rav Eliyashiv, one married woman who worked as a cashier in a store was taken by one of the Arab workers into his van, so the first time, let's say, it was onus, but the second time it happened, it's harder to say it was onus. So at the time, Rav Eliyashiv said that the husband has no problem because he is an onus, he doesn't know. But she is transgressing an issur de'oraysah each time she is with her husband (echad lebal, echad laboel). The mishna in the end of Nedarim says, if she tells her husband "I am tameh to you", the sugyah is mashma that if he doesn't believe her, the rabanan were mafkiyah the kedushin from them limafreiyah (which means they were never married, and so she isn't assur to him). Or, if he's a Kohen, in which case it doesn't help to get rid of the kiddushin because it was a be'ilas issur, for example with a goy, then there's a different heter (I didn't understand the jargon of this heter). So once she says she did something and he doesn't believe her, that sets into motion this heter of chazal of mafkiin kedushin. But that only helps if she tells the story, but if she doesn't tell her husband, we're stuck. She is being over an issur de'oraysah each time.
And the heter of techilaso be'onus vesofo beratzon doesn't apply in a case where she went, for example, to the forest with him. If a woman starts up with a guy or is ready to accompany him, you can't call that onus anymore (even if he ends up going farther than she had wanted).
But with all these cases, we'd like to prevent it from getting to a stage when it's going be too late. Now the truth of the matter is, for us - Am Yisrael - in general, it is better if these women stay married and someone watches them, and it's better that the husbands should stay married that somebody should temper him. Because if they get divorced, the woman is going to become mufkeres (having relations without going to the mikva, etc), and the husband will locate other women. And there are children involved as well, etc. So we'd like to try to avoid everything landsliding out of control. So what we'd like to try to do, is to try to send her a message that we know, and that she has to stop, but without letting her know how we know, in order that you can follow what's happening. But without destroying the marriages.
Now, regarding the son confronting his father and the issue of Kibud Av, on the one hand, perhaps if the father is an addict and he found out that help was available, he might take the help. But the son would need to find a nussach that is not pogeah in his Kavod, and also that won't send him underground, because then we won't be able to know if we need to keep vigilant. Perhaps the son could come home and tell his father than he heard a terrible story, someone in the community who is well known, with children and a good marriage, was caught having an affair. And somebody knows about this guy who tries to help people who are in trouble, his name is Yaakov, they don't know his last name, but he helps a lot of people, he has a website www.guardyoureyes.com and they say there's hope for these people, because sometimes these things are like an addiction... And then he could ask his father, "What do you think should happen in such a case?" In other words, letting him know that it's happening to people, and it's terrible what's going on, but there's help available. And what does he think someone should do in a case when something like this happens? Should they tell his wife, or try to get him to go for help? What's the right approach? He can say to his father, "I'm all broken up by what I heard, some people are upset, they went right away to his wife, it's a whole parsha. What would you say should be done in such a case?"
The father might get the hint that his son never spoke to him about these things before, that maybe he overheard something. But the son should play innocent. But maybe if the father hears this "story" it will shake him up a little bit.
We asked Rav Morgenstern again after the above discussion: If the son can't fake a story or doesn't want to, is he allowed to confront his father about it face to face or through a letter in a respectful way? The Rav responded:
He can speak to him or write him a letter, but not in an attacking way but rather like, "I am coming to you with tears in my eyes. I am afraid what will be with my father, with my mother. I am afraid for the embarressment of the family and children." He shouldn't make it sound like he is telling his father off for doing something wrong and that he must accept from him, but rather, "how do we stop this from continuing to slide? It will be so much better for everyone if it stops now". And of course he should let him know that help is available (SA groups, GYE, Therapy, etc.)