When using Aegir to upgrade production websites I follow a method very similar to the one outlined by Omege8cc – Safe Workflow
The safe workflow technique is nice as it lets you migrate sites into production without having to bring your live site down to basically test the migration. Occasionally, during the test migration Aegir reports that the migration has failed. However, if I look at my files it has successfully moved the entire site to the new platform but could not delete the settings.php file from the old platform and site. The important thing to check is that everything is now actually on your intended platform and is properly setup, vhost files, files dir, settings.php, etc…
If everything is peachy, Aegir did everything besides deleting the old settings.php file correctly. So, to clean up your Aegir interface you first want to delete the site that failed not using the delete button but by clicking the edit tab on the site and then in the URL changing the word edit to delete, and press enter. Confirm the deletion of the site.
Then on the server, delete the remaining old files off of the original platform. On the new platform navigate to your recently migrated site and change the file permissions on settings.php to 664. When you do your final migration Aegir will set the permissions back to the proper settings.
Next, go to the platform you migrated your site onto and verify the platform. Aegir will pick up the site, import it and you will be ready to finish your migrations.