I finally got around to, and succeeded in updating my and E’s VPS-hosted Mastodon instances.
For about half a year I wasn’t able to update Mastodon, because the automatically generated back-ups before the update were too big for the allocated disk space on the VPS. My VPS runs Yunohost, but the options in the web interface for admins are somewhat limited. One way to get around the lack of storage was mounting another disk, but that required command line access but I couldn’t ssh into my VPS because of a missing password. Making the back-ups smaller by deleting stuff from the database(s) also required the command line. I didn’t see a route out of that and in my burned out state these past 4 months I left it at that.
Today E mentioned she thought that her Mastodon instance was slow. Logging into my Hetzner account, where the VPS is hosted, I noticed that the type of server I have was being deprecated. I was invited to rescale the server. This was an easy option to add a bit of computing power, and extend the disk space. That done, I could update the Mastodon instances. So my need to find a way to the command line of my VPS no longer existed. That of course was the moment I noticed an option in the Hetzner interface to directly access the console of the VPS.
The Mastodon instances are up to date, I have enough disk space, and now know where to find the command line interface.