The baggage agent should be able to check your bags through to your destination, regardless of confirmation numbers. (Note that if you do have a single confirmation number this won't be an issue at all -- you'll even be able to use the kiosk to self-check your bags.) This does require additional effort on the agent's part, and I've learned that, following the system conversion, some agents know how to do this and are willing to assist without issue, and some others unfortunately are not. If you are polite, patient, and persistent you hopefully won't have a problem. Please do come back and let us know how it goes!
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