Perhaps I was too brief... or maybe I dont understand your post. Either way - I'll try to make it clearer.
I had added a "fully-hosted" sub-domain - admin.mysite.com and pointed it to the sub-directory on the server /home/username/mysite.com/administrator (that where the Joomla admin console is). Certain parts of the console weren't working properly (not sure why that is either) but they were all working fine before I created the sub-domain and so I figured I just needed to turn it off - which I did.
So the physical directory /home/username/mysite.com/administrator is still very much there and I used to be able to navigate to it by simply typing www.mysite.com/administrator, but now it (still) tries to re-direct to me to admin.mysite.com and then I get a 404 page.
Make sense? I just want to get rid of the admin.mysite.com altogether and go back to using www.mysite.com/administrator. (But it wont let me).