The Great Court in Jerusalem is the essence of the Oral Torah, etc.:

When the Great Court was in existence, etc., until one prohibits and another permits. A Baraita in Sanhedrin, chapter "Those Who Are Strangled" (Sanhedrin 88b): It is taught, Rabbi Yose said: Initially, there were not many disputes in Israel, etc., until the Torah became like two Torahs. The reason our teacher (Rambam) did not write that they should go to the court nearest to their city, as mentioned in the aforementioned Baraita, is because, since we are seeking a court to inform them of the truth, it is implicitly understood that they will go to the court nearest to their city before going up to Jerusalem. Alternatively, this was not in our teacher's version, which seems more likely.

Two sages, etc. In the first chapter of Avodah Zarah (page 7a), it is taught: If there are two [sages], one declaring something impure and the other pure, one prohibiting and the other permitting, if one of them is greater in wisdom and in number, follow him. If not, follow the stricter opinion. Rabbi Yehoshua ben Korcha says: In matters of Torah law, follow the stricter opinion; in matters of Rabbinic law, follow the more lenient opinion. Rav Yosef said the halacha is according to Rabbi Yehoshua ben Korcha. Since the first Tanna differentiates between someone greater in wisdom and number and someone who is not, it implies that according to Rabbi Yehoshua ben Korcha, even if one is greater in wisdom and number, in matters of Torah law, follow the stricter opinion, etc. Therefore, our teacher (Rambam) ruled in a general manner and did not differentiate....

What our teacher wrote about not in the time of the Sanhedrin means that if it were in the time of the Sanhedrin, we would not need this because, in any case, the law would be clarified, as mentioned above nearby.