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We have on Exchange 2010 server in our domain, on-premises. We added a second Exchange 2010 server in our cloud environment, which is also part of our domain and connected with a site-to-site VPN tunnel.

The goal was to migrate mailboxes to the new server and then decommission the old one.

After adding the second server, I made sure it was not associated with the Internet send connector. However, mail to external recipients continues to go undelivered because it is being routed through this new server, which isn't configured correctly. As a result, we end up getting delivery delayed notices on all emails to external users.

How do I keep this new server online and able to accept mailbox migrations, while making sure it is not being used for delivering any mail?

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Mail shouldn't be delivered to the second server if you have AD sites and services configured correctly. My instinct is that you don't.

As Exchange is AD site aware, it is important that you have the subnets applied to the correct site, so that Exchange and the domain controllers can see the correct site that they are located in.

Although personally I would be looking to get that second server setup for email delivery before you do any migrations. If your plan is to remove the original server then you will be doing that anyway, so why not do it now, before live users are on the platform so any testing doesn't result in loss of email.

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