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Thank you for posting your question. If you have machines in your machine group listed with both Hostname and FQDN, it will really only scan one or the other. It will not scan both machines.
For your situation, to make things cleaner I would say just remove either entry. As long as your console server can properly resolve a host name to an IP and FQDN, then it will be fine to just scan by hostname. The biggest thing to make sure is that whichever way you scan, Hostname or FQDN, the console server just needs to be able to resolve the name through DNS.
Hope this helps!
Thank you very much!