A while ago I booked a very sweet BRU-JFK-ATL-GRU-ATL-JFK-BRU ticket, all in business class for 2k USD.

Now I need to change the last leg (JFK-AMS), but since the booking class is low, they wanted to charge me 2k for changing the flight. I called a few times to see whether the cheapest rate really would be 2k, in the end it really was the case.
The last call was a bit funny. THe lady did a lot of work, she was clearly not happy when I didn't want to book the flight because she thought that I wanted to go ahead.
Now I checked my flight yesterday, and it turns out that the flight was added to my itinerary (I have wo JFK-BRU legs, a few weeks from each othter). It says that passenger is confirmed as well.

Could there be any chance that I could use both of these, how can I check whether the last/changed flight is really confirmed?

And finally, what would you do? Ideally I would like to cancel the original last leg and replace it, no clue whether that is possible though.