Actually, purchasing early is good, because it gives you the best deal. Flights do not change often, and usually the change is not a major change, although they are supposed to notify you, of any change. Also, it is rare that an airline suddenly goes bankrupt, like this situation.
If I were you, I would call AA, again. Inform them, again, of the issue. Ask them for the fare for the segment of the ticket that was on Aloha. Explain to them, that you are going to seek a refund/credit, for that portion -- through your credit card company, since Aloha went brankrupt. Ask them if they can send you a copy of the fare calculation, as proof, if you don't already have it. I would do this, incase the credit card company needs/wants to see this documentation. Call the credit card company, explain to them the situation. Explain to them the fare for the portion of the ticket that was on Aloha, then explain to them that Aloha went bankrupt, and you are seeking a refund/credit to your account, for that amount.
As for purchasing seperate tickets, to replace the Aloha portion. You can do it through AA, and it would probably be easier, and less hassle, but you can certainly do some shopping around, such as on Orbitz, and find a better deal, if there is one. AA can "sell" that portion into your itinerary, for checked bags, etc., at a later date, as long as you have your itinerary for that new flight, with the flight number/ airline, etc. Just let them know that you have another flight, on a seperate reservation, and that you need your bags checked all the way through, on that flights, and they can take care of it. -- I would only do that, if purchasing on a seperate reservation/airline is a lot cheaper than doing it through AA to begin with.
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