E-tkts are only "marked used" after the post departure entry has been done in ACI (automated check-in). If you don't board the flt your tkt is not marked used if it is an unrestricted tkt. Restricted fare basis tkts will be marked as "no value". I hope this helps. I also hope that you got the name of the res agent so you can forward your concerns to a CSM in res so they may revisit the correct policy with this person.

Thanks for flying CAL & Skyteam (June)