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Kevin, if I recall correctly, when you change the Custom SQL, as far as Tableau is concerned, that is a brand new data connection. that's why you can't do an incremental: you HAVE to do a full refresh first.
Then you will be able to do an incremental refresh, but not until the full load is done.
Is there a reason that you are doing this via custom SQL rather than a materialized view, or maybe even a Data Source filter?