Quite correct, apparently I need to take better notes when doing my admin duties
For anyone else that hits this (which is unlikely), what happened was:
I was updating some ssl certs on the same server via letsencrypt, and made a misstep or two during the setup and it put a directory in ~/frappe-bench/ called ‘.well-known’ which is used for verification purposes. I was unaware of that directory, and when running update, it tried to migrate it as an actual site, but the site was not listed, so threw that error.