Is there an option to not overwrite these files if they were changed by the user? Otherwise we could modify server.sh to call some "save/restore" script before and after.
I can understand that this contradicts the approach of ISPConfig - at the end of the day, it is there to allow you to avoid fiddling with these files. Another approach would be to probably not put the additional subdomains in the same, but in different .vhosts files that are not and have never been managed by ISPConfig, thus leaving ISPConfig out of that game entirely.
Am going to think about this for a bit. Thanks for the help.
P.S. Something that would be nice to have: A password change for the mysql root password. That password is stored in about 3million places, and for the appliance it would be great being able to change that with a single command.