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According to our description, we have a two-tier CA, one root CA server with multiple intermediate Enterprise CA servers. Now we want to decommission one of the intermediate enterprise CAs.
If so, we can refer to the following article to decommission a Windows enterprise CA.
How to decommission a Windows enterprise certification authority and remove all related objects
https://support.microsoft.com/en-gb/help/889250/how-to-decommission-a-windows-enterprise-certification-authority-and-r
But before we decommission one Windows enterprise CA, we should check all the certificates issued by this intermediate enterprise CA are expired or re-issued by other intermediate enterprise CAs.
Thanks