-your drive failed
-you ssh'ed into the machine and started a service that required the drive
-systemd put the system into emergency target
-you switched to the backup partition and systemd exited the emergency target
-the emergency shell is now inactive, but of course its output text remains on the screen
If that's a correct summary, I'm not sure what you wanted systemd to do differently?
So to summarize:
-your drive failed
-you ssh'ed into the machine and started a service that required the drive
-systemd put the system into emergency target
-you switched to the backup partition and systemd exited the emergency target
-the emergency shell is now inactive, but of course its output text remains on the screen
If that's a correct summary, I'm not sure what you wanted systemd to do differently?