The Yerushalmi says that a Chodesh is established by witnesses, and some girl has her third birthday on that Rosh Chodesh, she gets her besulim and can lose them with a man, but if later those witnesses were proven Zomemim, and we realize she was never three to begin with, nature follows the Torah and her Besulim grow back. This process is obviously not scientific but miraculous, and with no Kidush HaCHodesh until Moshiach comes, its going to be difficult for the scientists to observe the process.
Regarding the Rambam, Reb Yaakov Kaminetzky said that the Rambam’s Hilchos Deos were not intended to be Torah, but rather the Rambam’s secular wisdom. He said, by way of proof, that the Rambam there says the moon is a sentient entity, and now we “see” on TV that it is only a rock.
Rav Schneur Kotler ZTL said that this statement of Reb Yaakov “may not be said”, and that he remembers that Rav Meir Simcha of Dvinsk ZT’L once said that there are people who hold like this regarding the Rambam, and they are totally wrong, and he (Rav Meir Simchah) would really write a sefer showing that every word of the Rambams Hilchos Deos is culled from Chazal, but the Malbim already wrote such a Sefer so he doesnt need to. Rav Schneur continued, that nobody knew what Rav Meir Simcha was referring to by the Sefer of the Malbim until a few years ago (like 30 years ago from today) they reprinted a Kuntres from the Malbim showing that the Rambam’s Hilchos Deos was all from Chazal.
Rabbi Menachem Kasher (author of Torah Sheleimah) wrote a Sefer called “HaAdam al Hayareach”, where he devotes all of chapter 4 to this Rambam. He, too, quotes from the Zohar in a different place to support the Rambam: “Does then the ground so sentient? Yes, as it says (Mishle 3:19) ‘Hashem with wisdom founded the land'” Meaning, He created a land that possesses wisdom. He also quotes more. Rav Chaim Kanievsky also quotes sources throughout Hilchos Deos showing where in Chazal they come from.
About the Rambam and the Zohar, it is true, though not everyone concurs; the consensus is that the Rambam did not have the Zohar. Nevertheless, there are statements in the Rambam that have no source other than the Zohar (such as “Whoever gets angry is as if he worshipped idols”). The explanations given for this is that the Rambam had Medrashim that we no longer have, plus the Rambam was able to be “mechaven” to Kabbalah even though he did not have the sources.