an aside to your problem
I don't understand "so I can always get consistent columns"
Columns are part of the (metadata) DB structure with the backup JSON file having Library specific ways to recreate those (and other Library stuff)
User level stuff (what Libraries are in use, Plugins and other USER preferences) are in the configuration folder.
It has been awhile, but the installer did not stomp on existing configuration files.
So the question is. What are you doing (precise steps for an upgrade) that causes you to HAVE this happen?