I think you might onto something with the filesystem. I am using Hd-idle to switch off the HDD when not in use. It was of course in use the entire time during this, but I noticed in the logs that it came up multiple times as “assuming disk spun up after long sleep” even though it hadn’t been off at all.

Only saw this after I made my post and I cannot make sense of it, but I have never seen this message otherwise, it only happened during this period of not being able to access the server.