Tried calling again spoke to another agent for an hour, of which they were on the phone with the code share partner trying to work it out. In the end, same outcome, although they acknowledged that it "seems unfair" but that is their policy and the agent I spoke to did not have the "tools" at their disposal to fix the problem.
Recommended I email customer service, which i already have and sent the letter via Fedex today as well. Will post the response if/when i get one.
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