If you read the message carefully you might understand that you are trying to upgrade an 'OLD' version of a catalog a second time, - not the right thing to do!
Find the Catalog you upgraded to v12 previously by searching with Finder for .LRCAT files that have a -v12 suffix in the file name. They would be an 'upgraded' catalog (unless you renamed in the upgrade).
"Missing" folders and files are highly probable if you 'opened' an old catalog to upgrade.
DO NOT IMPORT ANYTHING! Importing will NOT fix this problem. You need to find your correct working catalog that was upgraded previously.
When you find the correct catalog - set your Preferences for the 'Default' catalog you want to open-
Regards. My System: Lr-Classic 12.3 Photoshop 24.5, ACR 15.3.1, Lightroom 6.3.1, Lr-iOS 8.0.8, Bridge 13.0.3, Windows-11.