I had problems removing a site in BlueQuartz due to an error on handlers/base/disk/clear_quota.pl failed
To fix this I had to turn off a number of things before starting
/etc/rc.d/init.d/httpd stop
/etc/rc.d/init.d/xinetd stop
/etc/rc.d/init.d/sendmail stop
Also swatch;
mv /etc/cron.d/swatch.cron /root

Turn off quota:
/sbin/quotaoff -ug /home/

Then backup and reset the quota database:

mv /home/aquota.user /home/aquota.user.bck
mv /home/aquota.group /home/aquota.group.bck

Then run quotacheck to get the quota back in sync:
/sbin/quotacheck /home/ -vugm

turn back on quota:
/sbin/quotaon -ug /home/
And than restore the values in the CODB database:
/usr/sausalito/sbin/disk_restorequotas.pl

Then when quotacheck finishes.
service httpd start
service xinetd start
service sendmail start
mv /root/swatch.cron /etc/cron.d/swatch.cron

Tadahh site could finally be removed.