It depends on whether the gate agent is up to speed or not. During very busy times, they may forget to check the waitlist, and flights may go out with empty FC seats.

I usually just say, "I just wanted to check if my FC upgrade had cleared", just before they call my row for boarding. As long as you're pleasant, and the GA isn't too harried, it often works out.

Once you board, there is only a slight chance they'll pull you out. (I'd guess 10%). Sometimes the scanner will "beep" differently when you're going through to let the agent know that your ticket was upgraded.