Absolutely no config files changed in between when this was working and when it wasn’t. I have over 3TB of free space, so that shouldn’t be an issue. rTorrent has never stopped running at any point and is still seeding, so it’s just ruTorrent that is unable to connect. The server didn’t reboot in that time, and no packages changed.
Having got the “No connection to rTorrent. Check if it is really running. Check $scgi_port and $scgi_host settings in config.php and scgi_port in rTorrent configuration file.” message, I checked the .rtorrent.rc file to see my SCGI port is 13126, and the ruTorrent config in /srv/rutorrent/conf/config.php says the SCGI port is 5000. I tried changing it to 13126 but that did nothing, and I’ve since changed it back.
I am currently on a Hetzner box running Ubuntu 16.04.3 LTS.