may want to review http://www.flyertalk.com/forum/unite...ne-flight.html
http://www.flyertalk.com/forum/unite...me-flight.html
http://www.flyertalk.com/forum/unite...me-flight.html
http://www.flyertalk.com/forum/unite...them-both.html

If this is not the last segment of the paid trip, not using the economy ticket will cause the rest of the itin to be cancelled.

If the paid ticket is a normal discount fare, the ticket needs to be cancelled prior to "scheduled" departure time to retain any future value.

A potential problem is the system determining there are two tickets for the same person and auto-cancelling one.

probably best to handle followup Q&A in one of the above threads since this is no a simple issue.