You should be able to delete/move everything other than Uncategorized… the error you were getting on upgrade appears to be related to some recent search performance changes.
There was a commit made yesterday that sounds like it might help avoid the issue you ran into (I’m not a backend developer, just connecting the dots)
Thanks for “connecting the dots” and yes, I made changes to all of them again (despite Uncategorized) and another upgrade worked without the same error.