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During the deployment of Sharepoint 2016, I added the smtp service to my WFE server. When I go into Central Administration, I see this server listed twice. Once by Netbios name with all Sharepoint services configured, and once by FQDN which shows Not Configured. See picture below. When I drill down into the server with the FQDN, I find that the service it provides is "Microsoft SharePoint Foundation Outgoing E-Mail"

Fast forward to today and I have installed some backup software for Sharepoint. This software is failing to backup this particular server. Each server in the farm is listed in the backup console with a Netbios name with the exception of this server. This server is listed by FQDN. The backup software vendor is telling me that this is the issue with the backups. In order to fix this, I added the smtp service to another external server and configured Sharepoint to use this new server. Now in Central Admin, I see this new server with the "Microsoft SharePoint Foundation Outgoing E-Mail" service assigned to it, and my original server with nothing assigned to it.

I want to click the remove server link from Central Admin to remove the FQDN name but I am not sure if this would cause any issue as it is still the WFE server listed in Central Admin with a Netbios Name. How can I remove the FQDN entry from the farm topology without affecting the services running on that server? enter image description here

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I have done a test in my SharePoint 2016 and i can reproduce your situation.

Once i configured outgoing email, use FQDN in the Outbound SMTP server, this server will be listed twice.

I click the remove server link from Central Admin to remove the FQDN name, it just remove the FQDN in the Outbound SMTP server, it has no effect on the WFE server.

Since you has added the smtp service to another external server and configured Sharepoint to use this new server. You can click the remove server link from Central Admin to remove the FQDN name, this has no effect.

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