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Is it possible to imput an excel file and keep the formulas in worksheets and that this formulas appear in the excel output file ?
Are the formulas consistent? Can you re-create them and calculate within Alteryx, rather than doing it in Excel?
If they have to be performed in Excel, you could use an approach like Writing Formulas to Excel in order to output formulas, though I'm not sure of a way to keep formulas on the input side.