score:2
I'm a Global Entry member, received a new passport, entered it into the portal online before my trip, and was able to use the kiosks without any problems. I'm a US Citizen, though I know of no reason why it should be different for a foreign national, unless you've done something like changed your name.
I can't see why you shouldn't try using the kiosk, since you're a member and you paid for it. At worst, it comes up with the "X" on your slip because your visa is in a different passport, and you have to speak to someone to get it resolved. The line for people with Global Entry issues is usually much shorter than the general visitor line though.