If I understand you correctly, you are not asking on Tosfos' question. Tosfos establishes that the Malkus that Edum Zomemim receive is in the place of the punishment that the accused was supposed to get and is considered Edus she'Atah Yachol l'Hazimah.

Tosfos then questions this premise: Why does the Gemara in Sanhedrin consider the testimony against Na'arah ha'Me'urasah to be Edus she'Iy Atah Yachol l'Hazimah since the witnesses in that case do receive Malkus?

Rather, what bothers you is why does the Gemara say that Na'arah ha'Me'urasah is not put to death becuase it is Edus she'Iy Atah Yachol l'Hazimah? The wording of the Gemara implies that they testify but Beis Din does not accept what they say. It seems that Edim of Na'arah ha'Me'urasah cannot give any testimony at all!

I think that the answer is as follows. The Gemara there says that the Edim are not put to death only when they did not warn her that she will be put to death if she goes through with her intentions. However, if they warned her that she will be Chayav Sekilah, then it is Edus she'Atah Yachol l'Hazimah.

Accordingly, it is understandable why they do come to Beis Din and testify. After their testimony, Beis Din asks them questions concerning exactly what happened. At the point when the Edim tell Beis Din that they did not warn her that she will be Chayav Sekilah, Beis Din does not accept their Edus.

In short: You asked, why does Beis Din let the Edim of Na'arah ha'Me'urasah come to Beis Din at all? The answer is that since there is a possiblility that Beis Din will accept their testimony, they come forth to testify.

I hope that this clarifies things for you.

Shevach Pepper