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The result of these being overwritten will be WHM showing "unlimited" quota reports for all users in the system. An quick solution to this is to run these commands from within the VE as root:
<pre>
rm -rf f /aquota.user 2>/dev/nullrm -rf /aquota.group 2>/dev/nullunlink /aquota.user 2>/dev/nullunlink f /aquota.group 2>/dev/null
for x in `find /proc/vz/vzaquota/ | tail -2 `; do ln -s $x / ; done
</pre>