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I suggest you to choose SSIS Package because SSIS is meant for such tasks. Well, for accessing file from other/remote server , you can use .NET Impersonation. It gives you a "Run As" capability in your code. If you Google you will find  cut & paste code that you use with SSIS script.Using .NET bilkupload/Bulkcopy is not bad but using SSIS is right choice.

In SSIS " Script Task" you can write simple logic for column differences and make it work"

Best Regards
Shabir Hakim, Dec 20, 2014
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