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There comes a time in everyone's security life you need to rebuild a cpanel server.. i'm talking about the OS, whm/cpanel and it's modules.. not websites. I wanted to document the process I use to rebuild it:

  1. Force an CentOS/Redhat Reinstall by:
    1. Create an empty directory: mkdir /tempreinstall
    2. CD into the new empty directory: cd /tempreinstall
    3. Force a Yum update: yum reinstall *
    4. delete the temp empty directory
  2. Force cpanel to update with:
    /scripts/upcp --force
  3. Force the webmail systems to update with:
    /usr/local/cpanel/bin/update-roundcube –-force
    /usr/local/cpanel/bin/update-horde –-force
    /usr/local/cpanel/bin/update-squirrelmail –-force
  4. Reinstall MySQL:
    /scripts/mysqlup --force
Your mileage may very, and you may run into issues on the OS reinstall.. so backup first.