I can't say what is causing your issue before the reboot.. other than Pi3's have kinda crappy USB so it's possible the drives are losing their connection for some reason, could be drive issues. I'm just not a fan of SBC's for this stuff (but I do think they have their place, just not as an always on media server)
Regarding it being gone after reboot, There's a good chance docker is starting before your USB drives are mounted.
To verify... Reboot your server (or if it's up now and jellyfin isn't working)
SSH the server and as root or sudo run this command
systemctl restart docker
The situation appears to be the same after the jellyfin setup and reboot.
Found it here
The link provides useful information, due to the fact that I think that the problem the user has is somewhat relatable to mine, so I'll read it more thoroughly. I applied the script and it does its work (starts Docker later on), but as I said before, the media server app is not configured, so I'm not able to see its utility.
EDIT: I did the same having created the container, and the results do not change.