List Virtual Servers missing virtual servers

I have 3 or 4 virtual servers that are missing out of the virtual server list and dropdown

they are functional however
user exists in /etc/passwd
files and link exist in sites-available and sites-enabled
sql users and databases still exist

I have found a connection to each server that has gone missing, essentially I created template virtualserver backed it up as a single file from the virtualmin interface. then proceded to rename the domain
Old domain name
New domain name

Change administration username selected
Automatically chosen name
Change home directory
Automatically chosen directory
Change user name suffix and group
Automatically chosen

then I would manually create a mysql user and mysql database change some php configurations and viola clone of a website
the listed server name even was changed in virtualmin

then I would load the backup to get the old one back
after that not sure if right after the other side would disappear out of the list.

I can not do this in the future but how do I correct the sites I previously created ?