Split into two itineraries by gate agent without my knowledge

Hi everyone. I am curious if this has happened to you. My girlfriend and I traveled yesterday with one layover in DCA. We return back next week. We were on the same booking code on a Basic Economy fare (w AAdvantage Plat benefits).

In DCA, I was offered an upgrade and I passed it to my girlfriend, who does not have AA status but was on my same itinerary, so she was registered for the upgrade list. I asked the agent if I could keep her window seat, as I didn't want them to fill it with someone and I'd still be in my middle seat. She said yes, she would just move me to the window and her to FC. I saw in my app that we were both present on the trip page with our new seats. All felt normal.

When we landed, I noticed that my girlfriend had disappeared from my trip page entirely. Like, totally gone from every leg, already completed or not. I was concerned, as I intended to take a flexible change offer to extend our trip by one day I called into AA; I learned that the gate agent in DCA split us into two itineraries when she upgraded my girlfriend and not me. I have all of the information for her itinerary and can access it in the app. I was able to use the flexible change offer to get us both onto the new flight, which is good. The phone agent informed me there was no way to add her back.

Now, I am concerned about a few things:

1. I want us to sit in MCE, I had to pay for her seats as it wasn't recognizing my Plat benefits. I am of the expectation that American should refund this. I paid as I wanted to avoid seats filling up.
2. She will probably have boarding group 9, which makes me think we will have to check our carryon. Given everything that could go wrong there, not optimal.
3. If something affects our travel, we may get booked on separate flights once changed instead of kept together.

Has anyone ever encountered something like this? What did you do? Any tips? I'm so frustrated that a complimentary upgrade turned into a headache.

Thank you in advance.