When I did something similar, I ended up with an issue because I had files in the home folder on the root partition conflicting with the files in the mounted home partition. I had to liveboot in and delete the files in the main partition so that the home partition would work properly. Could it be something like that?
No, somehow the settings were lost and my Deja dup back-up failed (the external disk died on me when I needed it) My files weren’t lost, though, just the settings and passwords.
Through Firefox sync I retrieved the passwords and I’ve created new ssh keys for the servers, so it is solved now.
Each time i hear about dead backup…well that’s just too much
No one is safe!!!