Copy Configuration A to be Configuration B.
Change something in B (e.g. Show Line Numbers).
Select B to be the current configuration. (!)
Copy A to be B again.
You’ll find the new B does not appear as A, but appears as the old B, as if you didn’t delete it.
And a suggestion:
I hope clicking Select button in Define Configurations dialog won’t close the dialog. This will be convenient for deleting/renaming the current configuration.
A configuration cannot be deleted when it is in use. I will try to reproduce your issue when I have a time. Thanks!