I had a similar problem so maybe ....
During your last update the permission of your /var/named/chroot/var/named directory have changed so the ISPConfig manager defaults to another direcory since it does not have access right anymore and saves the new zone file in that default directory
falko gave me the solution here :
chmod 755 /var/named/
chmod 775 /var/named/chroot/
chmod 775 /var/named/chroot/var/
chmod 775 /var/named/chroot/var/named/
chmod 775 /var/named/chroot/var/run/
chmod 777 /var/named/chroot/var/run/named/
ln -s ../../ chroot
chkconfig --levels 235 named on
then redo your DNS modifications ...