I run WP 3.6 MU with a few subsites on subdirectory structure.
All works fine, until I go to Sites > Edit site "x", change domain from networkdomain.com/site to subsite.com.
The site is fully accessible using the new domain, including pages, posts and other site areas. Except for wp-admin. No matter if I try to access thru the Network admin or directly from the frondend, WP directs to "comsubdomain/wp-admin". If I try to access wp-admin directly by typing subdomain.com/wp-admin I am redirected to comsubdomain/wp-admin as well.
Tried several things including network deactivating domain mapping. Also tried changing back the site url to networkdomain.com/site but that gives me a 404 on the frontend and a redirect of wp-admin to the mastersite admin panel.