Nittel is actually a great example of a Minhag that was around long before it was written. Chassidim value Mihagim and kept it. Yeshivos let it pass and get forgotten. The Chassam Sofer discusses it, as a Mihag he had, and quotes his Rebbe on it. The Mekor Chaim mentions it as a topic on his table of contents, although we don’t have the content.
A Minhag only gets into a Sefer if something came up. The Maharil is one Sefer where a Talmid decided to write down his Rebbe’s Minhagim. We get hints of Minhagim from side references quite often. What was the Minhag of the Baalei Tosafos to eat on Purim? They don’t write it to let us know, but they do discuss the Bracha.