Hello,
Thank you for posting here.
We could decom the Root CA if it will not be used anymore. It is Okay to do this if the issued certificates have already expired.
How to decommission a Windows enterprise certification authority and remove all related objects, we could refer to:
https://support.microsoft.com/en-us/help/889250/how-to-decommission-a-windows-enterprise-certification-authority-and-r
For any question, please feel free to contact us.
Best regards,
Hannah Xiong