This is just a short lesson's learned I want to share regarding the decoupling of a multi-site Drupal installation. Some of you know that there is a site called http://groups.idcminnovations.com. What you wouldn't know is it has been running off the same Drupal installation as this site. Makes sense I suppose given it is a sub-domain of this site. On June 9th, 2010 I migrated a copy of this Drupal installation to a separate site on our server and redirect the groups server alias to its own Drupal installation. Sounds simple enough - it's been done before. When the copy was made, for some reason the .htaccess file content disappeared. You could see the file on the server but it was empty.
The error message read: "Not Found - The requested URL /articles/setting-drupal-organic-groups was not found on this server." when I tried to access a node on the site. My heart stopped beating for a second. I contacted http://prohosters.com and the guys went to work. Within a minute, Marius found the problem. He copied the .htaccess directory from idcminnovations.com into groups.idcminnovations.com and I was back in business.
So, the message is be careful when you copy. The contents in the .htaccess file allows the server to understand Drupal's virtual pathing structures. I don't know what prevented the .htaccess contents from being copied in the first place but if this happens to you, now you know ;-)