A vendor of ours cannot guarantee the flat files column order. How does the Flat File Connection handle when the columns are rearranged?
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The Flat File Connection will not rearrange the columns if they appear in a different order. You will have to load the data with headers and reorder them dynamically, either using SSIS or a database.

Alex
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how do i load them with headers? do i uncheck "column names in the first data row" and use script task to find the first row and remap in code? – vin Mar 20 '15 at 22:25
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Yes, you need to uncheck "column names in the first data row" and make sure you start the import at row 0. You could use a script task to reorder the rows and output the data to a intermediate file. Alternatively you could use a combination of an unpivot and pivot to reorder the columns. – Alex Mar 20 '15 at 22:43