The very first thing to do as @Stephen Ostermiller points out is to do a full backup of all your configuration settings. Now having said that if you do an in place upgrade from Server 2012 to Server 2016 then you won't lose any configurations except for those that are no longer supported or needed within 2016.

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: Will upgrading Windows Server 2012 R2 to 2016 lose all configurations? I want to upgrade my AWS EC2 instance to 2016 to make use of Docker containers. Will I lose my 2012 Server configurations

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