Just make sure that CIC1 is running as the Primary server. Take CIC2 offline (or put it on a network segment where it cannot communicate with CIC1).
Rebuild CIC2 from scratch to fix the OS, making sure the OS ends up on the same version and Microsoft patch as CIC1, using the same computer name for the server as before, same IC Admin account as a Local Administrator...everything as outlined in the IC Installation and Configuration Guide.
Install IC per the Installation and Configuration Guide, and make it the other server in the Switchover configuration when it comes to that point, after setting the Site name to be the same as CIC1.
Just be sure to follow all the directions for installing the switchover server very carefully, and when it comes up as the backup it will replicate all the configuration data from CIC1.
You will be running without a switchover pair the whole time you are rebuilding, so do it during a down time for the call center if you can.