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Hey Craig -
As I understand it, you created an extract and published that to Tableau Server where it is refreshing automatically, right? You're still using the "local" version of this data source of this machine for your Desktop work, however.
Why don't you publish the data source & extract (NOT the workbook itself) to Tableau Server as a Tableau Data Source instead? Put it on a scheduled refresh, too. Then, you can use it as a data source right from Desktop - and you don't have to worry about the local refresh any more.