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Helpful advice for re-issuing any unsynched tickets:

a very friendly agent this morning was having trouble re-issuing mine when there were no schedule or flight # change present.

When I explained to her that a confirmed upgrade had been cleared by PMUA as a result, she instantly told me that now she knew what to do- and cleared it out.

So let your agent know about the "class of service change" for the reason this needs to be reissued. Best of luck!