I had a very similar issue, albeit with a different airline. My first segment was late and an agent at the connection airport thought I was going to misconnect (last flight of the night) and proactively rebooked me on a flight the following morning. I didn't misconnect (and knew nothing about the rebooking) and made the flight with seconds to spare. BP scanned and I boarded and flew. I was overnighting in the next city with an onward flight the next morning, which I also flew with no problem. The app showed my return 8 days later as totally normal. Until I tried to OLCI.

I got a message to call in and I was told I had no showed on my outbound so my return was cancelled. I said I absolutely did not no show and was in fact at the destination waiting to fly home the next day. We finally realized we were talking about two different outbound flights and, after some digging, they pieced together what happened. To this day, they still can't figure out how I flew 2 further flights after my 'no show', including one the next morning. Plus, the miles from the actual flights I flew had already posted to my account - further proof that I actually did fly as booked and the thing that finally convinced the agent.

The point is, everything looked completely normal to me both on the app and the website right up until I tried to check in at T-24. I even took a screenshot as the agent didn't believe me as she could clearly see the flights were cancelled. Something in their system did not update my res with either the 'no show', the new flights (that I didn't take) or the cancellation of my return flights. And this was all on one airline - ticketed and flown on their metal. So it isn't surprising that this could have happened, especially as C-W-S says, when you are sharing info across different systems.