FWIW, I've had no problems calling the elite desk and being protected on later flights when connections were at risk.

This is why you should allways allow 2 hours between connecting flights..any airline website will sell you a shorter connection..BUT..YOU need to plan ahead and understand delays are possible and allow yourself some extra time between flights..It will take the pressure off running to the next flight and will most likely help you get to your destination the sameday..(and maybe have time to stop at the PC along the way)..I go out of my way to book odd connections that allow me extra time and its reduces alot of stress..just a thought..@:-)@:-)

This is where you went wrong.

You need to look at the reservation BEFORE getting any human involvement. CO's computers are EXTREMELY good at protecting people for possible misconnect situations (and you know I don't often compliment CO's systems).

When the situation turns shady, and you are approaching a possible misconnect, CO will autoprotect you on another flight or route. This is done, all while keeping your original flights (exactly what everyone posting here wants to be done).

Once you're in the air, and it looks like you're going to make it, the protection disappears. Similarly, once you misconnect, your original flight disappears. It's very straightforward.

Most of us never know this is happening since we're not checking our reservations repeatedly while in the air. Similarly, when we do misconnect, and approach an agent for rebooking, they act like they're putting you on a new flight, but in reality it's already been done, they're just resynching the ticket and printing a BP. But if you ever have a friend/companion flying, and you watch their res like a hawk, you'll see some cool stuff pop in and out of there if there is a potential misconnect. You really don't need to talk to anyone unless you don't like the new options (e.g., it is still a computer...if the next open flight to MDW is not for 2 days, but ORD has space in 2 hours, it won't change the city for you, but a human can).

Anyhow, I'm willing to bet that CO did the same for your wife, but when she went up to the GA to protect herself, the GA figured she probably wouldn't make it (or was under some directive not to double book people), she just picked the likely conneciton (the later one) and left it at that.

The fact that your wife did not have a BP to her original connecting flight quite likely validates what I'm saying. If she were on the original flight, but protected on the second flight, she would have been carrying a BP for the earlier flight, but not the later. Instead, she had the reverse. So I'm thinking the agent gave her a BP to Flight #2, and if she made Flight #1, and there were still space, she could switch back per the note. Meanwhile, CO probably rerouted her bag to Flight #2. She should have asked for a BP for Flight #1.

So, in retrospect, 1) check the record online before requesting changes, and 2) do not surrender the BP for the original connecting flight. If they ask for it, there's something up. You always want to fly as confirmed until it's a sure thing that you're going to miss.

Sorry to hear about the mishaps. Sometimes things work better if they're left alone...

The counter agent wanted to rebook her for later flight, that is when I got called. My instructions were plain to the wife but the counter agent went and did just as she was going to do as if the wife never had called me.

It was CO human induced, no doubt about it.