There are no known issues with running SmarterTrack on Windows Server 2016.
I would suggest performing the migration first, and then upgrading to the latest release.
Instructions to perform the migration can be found in our knowledge base here: https://portal.smartertools.com/kb/a2581/move-smartertrack-to-a-different-server.aspx
Once the migration has been completed, you'll want to follow the instructions in our KB article here: https://portal.smartertools.com/kb/a2620/upgrade-smartertrack.aspx
I hope this help.
Technical Support Specialist / Internal IT