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I understand there is already an existing Autodiscover record for your on-premises organization. Since the hybrid deployment is between the CAS role in the hybrid server and Exchange Online, changing the Autodiscover record to the hybrid server is to make the configuration wizard detect services in the hybrid server correctly. Otherwise, some of the hybrid feature will fail in the deployment process.
If your long term goal is to move all the mailboxes to the cloud, I just recommend you to set up a standard Hybrid environment by referring to the Exchange Hybrid Deployment and Migration with Office 365 and the Exchange Server Deployment Assistant. As far as I know, the hybrid server license is free and which is dedicated for Exchange Hybrid Deployment with Office 365. Unfortunately, it is not allowed to move the CAS/HT roles to the hybrid server.
Ok, so basically your saying we can't move routing, OWA, or ActiveSync to the hybrid server? I am fine with that as it sounds like it would be a headache to do it. I have been following the deployment assistant, but thought maybe a couple of the services could be moved over to the hybrid server. I was just concerned with the FQDN's on the servers and how that would work to change them, but since we can't do it I'm good!
Now the question arises that if the hybrid server cannot be used for these roles why is it required, by the deployment assistant, to set the Autodiscover record up to point to the hybrid server? Why wouldn't I leave the autodiscover record pointing to the on-premis CAS server?
Thank you! I believe I am starting to understand the hybrid server role better.