I’m running a coexistence scenario with Exchange 2013 and Exchange 2016 without too many issues. My hybrid server is running on Exchange 2013 from the beginning, and it is time to upgrade this server to Exchange 2016.
If you have configured your Exchange environment correctly the hybrid server is nothing special. In my environment the hybrid server is just used for sending SMTP messages between Exchange Online and Exchange on-premises, and it is used for migrating Mailboxes back and forth.
Upgrading the existing Exchange 2013 hybrid server to Exchange 2016 is actually just a matter of installing a new Exchange 2016 Mailbox server, configure it correctly like the old Exchange 2013 hybrid server and rerun the Hybrid Configuration Wizard application.
Figure 1. The new hybrid server (hybrid02) will be installed next to the old hybrid server (hybrid01)