vhost.d/* set back after adding new domain

[Cheecoh]

Is it possible to change my documentroot for a subdomain permanently?

i'm using a framework with the following structre:
/dirA
/dirB
/dirPublic
/dirC

in /dirPublic/ is my index.php...
/dirA - not accessible by web
/dirB - not accessible by web
/dirC - not accessible by web

till now i tried the way to change my apache/vhost.d/*.conf to use the correct DocumentRoot but now i've added some new domains and the conf where overwritten...

What's the beste way to avoid it? I've also tried to use a Symlink, but it doesnt work correctly as supposed :/