XenMobile: How to migrate the Cert Based Auth from existing CA to a new PKI-Infrastructure (With a new Root CA and Issuing CA)?

Existing working two-factor-authentication for XenMobile using cert based auth as the second factor are XenMobile-certificates that are issued by a Windows Enterprise Root CA. This Root CA will be decommissioned and replaced by a new Windows Enterprise Issuing CA that is signed by a new Root CA...