Apache service reset config on reboot

Hi to all,
i upgraded one of my servers from SnowLeopard Server (10.6.8) to 10.9.4 Mavericks Server, all services migrated fine
except for Web Service, in this case i needed to rewrite in every virtual host file <mod_rewrite> and <Directory> sections because
some of these setting didn't migrate in new config files (Now under /Library/Server/Web/Config/sites instead of "classic" /etc/apache2/sites).
The problem is that OsX doesn't keep modified settings in config files after a reboot so i need every time to rewrite them.
It seems that OsX restore them to "default" deleting only <mod_rewrite> and apache "basic authentication" inside <Directory> section...
Taking a look at logs didn't help because there isn't an error related to apache. I tried also to to run "apachectl -t" but syntax is OK..
Any idea?
thank you

Put your stuff in a separate file and place an include directive in the apple managed file.

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