Sub server mail users missing after migration

I've been using VM2 (Scott Grayban is my server admin and created an account for me on his server) to migrate a domain (server) that contains sub-servers from one Debian machine to another and have noticed that the alias' Apache config files are not removed properly on the source server which results in Apache not restarting properly. I had to manually remove the config file and restart Apache.

Status: 
Closed (fixed)