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Hi Jason,

You can make use of the EnsLib.EDI.X12.Document property SegCount, which keeps count of the number of segments in the document.  In the Data Transformation, you can add an assign action after all of the segments have been added in order to set the value of the SE01 element.  To do this, you should set the 'Property' of the assign action to target.{SE:NumberofIncludedSegments} and set the 'Value' of the assign action to target.SegCount.

Hope to help!

-Kimberly