Rashi says that if Beis Din tells someone to cover the blood of a Koy, the person himself will think that it is surely a Chayah.
My question is, surely Beis Din must tell him not to bless on Kisuy ha'Dam because it is a Safek!
P. Feldman, Yerushalayim
That is an excellent question, and it is asked by the SHITAH MEKUBETZES in Beitzah here. (The only other Rishon or Acharon I found who discusses your question is the SIMCHAS YOM TOV of Mahar'al Tzanz.) Here are some possible answers.
(a) The Geonim and Rishonim were divided as to whether one makes a Berachah when performing a Mitzvah due to a Safek d'Oraisa. Halachically, the RA'AVAD rules that one does while the RAMBAM rules that one does not (Hilchos Milah 3:6 and many other places). Your assumption is based on the ruling of the Rambam, which was adopted by the Shulchan Aruch (OC 67 and 688), not a make a Berachah on a Safek. It might be pointed out that strong support for the dissenting opinion, which requires a Berachah even for a Safek, may be brought from our Gemara.
(b) The Shitah Mekubetzes answers the other opinion as follows (as I understand him):
Your question may be reversed. The Gemara says that if a person is told to cover the blood of a Koy during the week, he will not infer that a Koy is a Chayah. Rather, he will tell himself that even though the Koy is a Safek Chayah, the Rabanan required him to cover its blood out of doubt. Why would a person come to such a conclusion? Wouldn't it be more logical for him to conclude that the Rabanan consider a Koy a Chayah -- and then to be led to the mistaken conclusion that its Chelev is Mutar?
The answer to this can be found in your question. The Rabanan will certainly tell him not to make a Berachah on the Kisuy, and this will arouse his suspicions that the Koy is not an absolute Chayah. This is why he will assume that the Rabanan told him to perform Kisuy out of doubt and not out of certainty. (In fact, the ITUR learns like the Ra'avad, that one normally makes a Berachah on a Safek, but when it comes to the blood of a Koy he rules that one does not make a Berachah on the Kisuy - lest one permit its Chelev. This is apparently based on the Gemara's statement that the Kisuy of a Koy's blood during the week will not be misleading.)
If we tell a person to perform Kisuy for the blood of a Koy on Yom Tov, however, a person will become convinced that the Kisuy is a "real" Chiyuv, and the Koy is an absolute Chayah even though he is told not to make a Berachah on the Kisuy. It is so unusual to permit one to carry dirt on Yom Tov, that one will assume the Rabanan would not allow it for a Safek Chayah, and the Koy must thus be an absolute Chayah. As for the Berachah, he will assume that not making a Berachah is an added "Chumra d'Rabanan," even though the Koy is really a Chayah. (Perhaps he will reason that this Chumra was instituted so that people should not think that one is required to make a Berachah on a Safek d'Oraisa, since a Koy looks like a Safek d'Oraisa even if it is a true Chayah.) Thus, people might become convinced that the Chelev of a Koy is permitted, and that it is a true Chayah, even though they are told not to make a Berachah on its Kisuy.