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I have a fairly complex workflow associated with a library of Excel files. I need to be able to add a time stamp to the bottom of the file when the workflow is finishing up.

Most of my previous experience with editing Excel files is querying via a Odbc connection. As far as I can see, there isn't a built-in Sharepoint ability to do so. I don't have file system access to just write the file to a temp location on disk. I don't know of any way to edit the Binary Stream that Sharepoint provides.

A: 

You could use the OOXML SDK to edit the binary stream of the Excel file and set that time stamp.
Take a look at OpenXML Developer.