Um, in order for changes in httpd.conf to take effect, Apache webserver must be restarted.
If httpd.conf was rewritten everytime Apache restarted, then it is impossible to make any changes to it, even for just 1 clock cycle.
httpd.conf would be quite useless, since Apache might as well store the configs internally, and refuse to let anyone change it without having to recompile Apache.
That in turn would make any binary distribution of Apache not very useful, since it would be better to simply get the sources alone (saving bandwidth), and compile Apache yourself, after altering the configs by altering the code.
My guess would be that he has another script that needs (or rather, wants) the webserver to be restarted every 15 minutes.
Whatever script was used for that purpose also wrote a new copy of httpd.conf
If that's true, then that script is probably a Bad Thing.