I have gone through this document to try to change the location of the Bitbucket home directory but it never changes. Do i need to uninstall/reinstall to change this location or is there something i am missing to get this moved for all users? This is a new 2016 windows server connected to a SQL database.
What do you mean by "to get this moved for all users"?
You are only trying to move the location of the application's data directory right?
As the document describes you need to change the path in either:
<Bitbucket Server installation directory
>\bin\set-bitbucket-home.bat script
I'm not a Windows expert but you might want to check the environment variables set for the user running the Bitbucket application and check the service configuration if you are running Bitbucket as a service.
If you run Bitucket as a service the value in the .bat file will be ignored. That might be your issue. Read more on https://confluence.atlassian.com/bitbucketserver/running-bitbucket-server-as-a-windows-service-776640048.html
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