On a Linode Virtualmin CentOS 6 the upgrade from Xen to KVM breaks quotas with the following error:
repquota: Cannot stat() mounted device /dev/root: No such file or directory
The issue is that the symbolic link /dev/root is linking to /dev/xvda which has been replaced by /dev/sda so the symlink just needs to be replaced:
# rm /dev/root
# ln -s /dev/sda /dev/root
Then pop into Virtualmin (Webmin, System, Disk Quotas) and turn the quotas back on.