Prevent Server.app from repeatedly hosing .conf files?

It seems every time I add or delete web server entries the Server.app replaces all my site .conf files, requiring a tedious manual replacing of AllowOverride from None back to All.  Is there some way to prevent it from altering the files for sites I didn't change, or a way to make All the default value? Very frustrating.
Thanks in advance!

Well, since apparently no one knows the answer to this, I'll share what I dug up today. 
In the /etc/apache2 readme.txt file (I'll be happy if/when Apple releases an actual Lion Server manual that covers all of this. If I wanted to play scavenger hunt through file systems looking for miscellaneous readme files to learn how to use software I'd have stayed with Linux where that sort of thing is in vogue), there is this little nugget:
=======================================
sites_disabled/default_default.conf
sites_disabled/0000_default_default.conf
This is the configuration file template for all new default virtual hosts created by the Server application. Administrators may modify it directly. (It is installed as default_default.conf and then is renamed to 0000_default_default.conf by the Server application.)
=======================================
So, I changed the 0000_default_default.conf file so the AllowOverride is set to All instead of None.  Now whenever I create a new site entry (or change something so that Server.app decides to rewrite all of them for me whether I want it to or not) at least now the default is sensible and I don't have to go back and edit them all again.
Hope that helps someone.

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