I am now having significant issues as well...I just did the same thing as you, I was using repo but it was not updating. I used the deb install and updated and I thought everything was fine...but I discovered, as you did, that the folder name changed from "emby-server" to "emby" that has caused all kinds of things in my setup to go haywire. I can fix all the things that are related to my shares, metadata updating etc. that goes on outside of emby...but now it appears that emby itself is broken as I am getting errors trying to scan the library.
From the dashboard it displays this...obviously because "emby-server" folder no longer exists. Other than doing a simlink, is there a way to tell emby that the folder name is different? I would have assumed that running the deb would have done a proper upgrade, which is what I read from a comment @Luke made in a post.
What to do next?
Scan media library failed.56 minutes agoCould not find a part of the path '/var/lib/emby-server/root/default/Movies - DS1817'.
I remember seeing a post with a similar problem to this in the test area shortly after the switchover to the pre-built packages. I think someone had gone through and made a symlink or something from the old folder to the new folder. I wish i could say i remember better what was done. For many i think its less problematic to backup everything, remove the old emby, install new emby and then restore libraries and such.