Comment 1 for bug 1334572

www.conf is a conffile. Deleting it should not replace it when the package is upgraded.

If updating manually, the following prompt should appear:

Configuration file `/etc/php5/fpm/pool.d/www.conf'
 ==> Deleted (by you or by a script) since installation.
 ==> Package distributor has shipped an updated version.
   What would you like to do about it ? Your options are:
    Y or I : install the package maintainer's version
    N or O : keep your currently-installed version
      D : show the differences between the versions
      Z : start a shell to examine the situation
 The default action is to keep your current version.
*** www.conf (Y/I/N/O/D/Z) [default=N] ?

Do you perhaps have the following option set up in apt somewhere?

Dpkg::Options {
   "--force-confmiss";
}