Hi Steven,

I am not in a position to answer your question fully, since the practical Halacha in cases like these are in the hands of Dayanim, who might use loopholes in certain cases. I can answer as far as I know.

In the Gemara you referred to, followed by the Mefarshim and Poskim (see Rambam Isurei Biah 15) it specifically says that although Min ha'Torah, a Safek Mamzer is Mutar, but Rabanan prohibited to use this Heter, because another extra reason - Maala Asu be'Yuchsin. We find this principle in a few places, that Rabanan were extra cautious to make sure no mistakes are made, since marriage and children are non-reversible, and the Yichus of Klal Yisrael is extremely important.

After the Rambam and the Shulcan Aruch accept this as Halacha, I cannot see how any contemporary rabbi, can just ignore these giants.

On the other hand, in complicated cases, there is no question that a Rabbi can refer to a Din de'Rabanan in a more lenient way than a Halacha in a status of de'Oraisa.

As far as your question from the Avnei Nezer I'll say over what he is trying to say, and then refer to your question.

As you know, the Rambam learns from the fact that a Safek Mamzer is Mutar Min ha'Torah, that every Safek what so ever is Mutar Min ha'Torah. The Rishonim argue and thousands of words were written around this Machlokes.

One of the questions the rishonim ask on the Rambam is that if every Safek is permitted Min ha'Torah, and the Issur in a case of Safek is just a Chumra of Rabanan, why does Rava need the special reason of Maalah Asu be'Yuchsin Let it be like any other case, that the torah permits a Safek Issur, and Rabanan came along and prohibited the Safek

To this the Avnei Nezer offers, that we need the extra reason of Yuchsin according to his understanding in the opinion of the Rambam, that if we say that a Safek Mamzer is Mutar, it means that until the issur is not clear cut, there is no Issur whats so ever, and she is considered Mutar as if there is no Safek. We can assume that the essence if the Chumra of chazal is that in a case of Safek, they do not want you to do an Aveira even if it is not sure, and even if Min ha'Torah it is Mutar, since at the end of the day, he might be doing an Aveira, so even though it might be permitted to do this Aveira in this case, it is still better to refrain. But if we say that a Safek Mamzer is as if there is no Issur, why should Chazal Machmir in this case, since there is no Issur at all in the case of Mamzer, until the issur is clear, so even if this person might be really a Mamzer, but this kind of Mamzer is not a Mamzer in the first place, so there is no reason to refrain.

To this Rava says, that the reasoning of Yuchsin is valid even in cases that there is no Issur at all, since the Maala of Yuchsin means that even a case that there is no Issur at all, we still want to be careful in the Yuchsin ballpark that no one makes any mistakes by seeing or learning from this case. Now, we can answer this way the question on the Rambam. The reason Rava brings is not why Rabanan were Machmir in there usual Chumra of Sfakos, but rather an extra reason they were Machmir even in a case the Safek has no potential Issur at all.

Now to your question. The Avnei Nezer says that according to the Rambam's opinion, in a case of Safek, WITHOUT the extra Yuchsin reason, that a person who knows the details and the Safek, can marry a Safek Mamzer mi'Deoraisa, but still, since Yuchsin is a very important matter, Chazal prohibited this not because he might be marrying a Mamzeres, since there is no Issur at all in a Safek, but rather because the Maala of Yuchsin.

I hope this helps, and somehow sheds more light on this difficult Sugya.

Best regards,

Aharon Steiner