The gemara says that R' Eliezer ben yakov holds that shinuy isn't koneh from the fact that he says if one steals wheat and converts it into bread, the bracha on hafrashas challah is "rejected" by Hashem. The gemara pushes off the proof - perhaps he holds that shinuy is ko'neh, but the bracha is rejected since it is a mitzvah ha'ba'ah b'aveira.
The Rambam (Brachos 1:19) paskens that one should not make a bracha on any forbidden food, regardless of whether he is eating it intentionally or unintentionally. Tosafos 67a seems to agree with the Rambam that regarding the bracha which mentions the name of Hashem, one should be machmir not to make the bracha. The Ra'avad disagrees, although one doesn't make a zimun on forbidden food, he does make a bracha. Our gemara seems to indicate that the Rambam is correct, that one does not make a bracha on forbidden food - the bracha is rejected by Hashem. How would the Ra'avad explain our gemara? The Rosh in Brachos sides with the Ra'avad and explains that the gemara doesn't mean to say that you don't make a bracha. Rather, the bracha that you make is disgusting in Hashem's eyes, but nevertheless one is required to make a bracha (and presumably it is more disgusting not to make a bracha). The kesef mishneh suggests that their machlokes may be pending on whether we have the girsa of "כיצד מברך", which indicates that there is a bracha.
R' Akiva Eiger (mishnayos brachos chapter 7) asks based on our gemara. According to Abaye who understood that the rationale for the bracha being rejected, is that it still belongs to the original owner so that the entire mitzvah isn't binding. Abaye is clearly understanding R' elazar ben yakov like the Rambam that he is saying one should not make a bracha, because the mitzvah of hafrashas challa isn't binding since the dough still belongs to the original owner. How can the Ra'avad and Rosh hold that one should make a bracha (just that Hashem is repulsed by it)? R' Akiva Eiger himself indicates that they will have to say that when the gemara pushes off Abaye and explains that shinuy is ko'neh, and the reason for the bracha being rejected is a mitzvah ha'ba'ah b'aveira, we are no longer compelled to explain that the bracha isn't made. R' Elazar ben yakov would hold that the bracha is made, just that since it is mitzvah haba'ah b'aveira Hashem is repulsed by it. Based on this approach we are forced to say that the Ra'avad and Rosh hold that there is a way in which one can fulfill the mitzvah even when it is a mitzvah haba'ah ba'aveira (such as Tosafos 67a quoting the R"i that whenever the kinyan is made before the mitzvah, he would fulfill the mitzvah, just can't make a bracha).