Yes. if she is a week queen or laying a lot of drones they will replace her. This is tricky situation, if you try to introduce your new queen and they have started supersedure cells they will more than likely kill the introduced queen..
You could check all frames and remove all queen cells, make sure you have no queen and wait 24 hour, then place your new queen in a push in cage to introduce her. That way she can start laying eggs right away. This way if they do kill her they have fresh eggs to start a new queen. I had two hives do something similar to your situation last year and they accepted the queen in one hive and killed the queen in the other but used her fresh eggs to replace her.
I hate to see you lose a new queen, how big is this hive. If it is really strong you may be able to split it. Leave the queen cells for the one hive, and shake half the bees for the new queen. You have to have a really strong hive to do that with and make sure you don't have any laying workers, or queens of any kind. Cells, Virgins, or old Queen, or want to be queen (laying worker/s) Good luck. Hope it all works out for you. Like I said, Tricky situation.