Is the extract refresh in question the one that Tableau Server is doing? What sort of data source is it hitting? You might want to review the Performance portion of Tableau Server Help for assistance to better understand what's happening under the covers. - Performance
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No worries you can fix this problem use below steps.
Download your published extract and open the same in Tableau Desktop and delete all unwanted field which you want to delete and overwrite the same with published one.
And try to refresh the same again.
But make sure you above steps will works only if your are using table directly in tableau then its fine other wise check your custom SQL code or view or Stored Proc and check whether these are having those columns which were adding to your extract automatically after each refresh. If they really exist in view/custom SQL/Stored Proc then please comment those files accordingly and republish the same and try to refresh it again you will get only those fields which you want now.
To clarify, I am building an extract that is created from a data source stored on my Tableau Server. These are valid fields for other workbooks, but not for this particular extract. The refreshes I was performing from the earlier in the thread were happening in Desktop and Server.
As was previously stated, this is more of a nuisance than anything else.