Using the setup wizard to upgrade an Exchange Server to a newer Cumulative Update causes an Exchange server to be marked offline in Exchange Active Monitoring during prerequisite analysis and prerequisite installation. If the setup wizard isn't advanced to continue the upgrade process, the server will remain in an offline state until the setup is allowed to proceed. Also, if any of the setup /Prepare* switches are used to update Active Directory on a functional Exchange Server, the server is marked offline in Exchange Active Monitoring.
This issue occurs because the setup puts the server in an offline state before the binary upgrade process is ready to proceed.
The setup will delay and make a server offline until the binary upgrade process is started.