Also, when the ticket is re-issued, the SWU should disappear. To re-issue, you should ask to be sent to the skyteam desk. I do agree that sometimes, the agent will do the booking and process the upgrade but the problem appears later when you the ticketing desk can't or won't re-issue the ticket. Call ASAP and ask for re-issue.
Please keep us updated as being able to upgrade delta W fare using SWU is really a great benefit that should stick!