Backups without home directories

I am going to perform my system upgrade tomorrow and just completed a test run of backing up all the sites.

One problem has occurred with alias servers that don't have a home directory with the "one file per server" style backup. These domains don't get backup.

Choosing the one file for all will be too big and susceptible to failures/hard to debug etc.

It there a way to backup an alias regardless of the presence homedir?

If this is not possible, is there a way to run the back only for sub-servers into a single file without needing to figure out which domains are aliases?

Status: 
Closed (fixed)