it depends on your infrastructure workflow procedures. The best way is to:
Prepare, set up and configure clustered CA.When you ensure that it works as expected, you can remove all templates from the 2nd CA, so it will not issue any certificates.Dump 2nd CA's database for any valid (time valid) certificate to identlify cert holders. If active certificates were issued to offline users and/or computers (which are not members of your Active Directory forest), then you will have to reissue certificates
to them first. If active certificates were issued to domain computers and manual enrollment was used (manual when you supply subject information during enrollment, like you enroll for SSL certificates), you will have to reissue certificates to such servers
too. If certificates were issued by using autoenrollment (automatically), you can revoke them and autoenrollment trigger automatically detects this and reenrolls certificates from clustered CA.Only then you can start CA decommission process:
http://social.technet.microsoft.com/wiki/contents/articles/3527.how-to-decommission-a-windows-enterprise-certification-authority-and-how-to-remove-all-related-objects.aspxMy weblog:
http://en-us.sysadmins.lvPowerShell PKI Module:
http://pspki.codeplex.comWindows PKI reference:
on TechNet wiki
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