It will come back for at least one game. There are plenty of Duke Fans who still love the character (I am not one of them, but everyone has their own tastes), but did not like the shoddy excuse for a game that DNF was - jeez, FOURTEEN YEARS of work and THAT'S what they make? Inexcusable. However, Gearbox, an actual competent developer, has the right to make more Duke Games now. Gearbox only patched together DNF out of the garbage that 3D realms released. While I don't think Gearbox should have released garbage, when it was clearly garbage, they weren't responsible for the mess that DNF was - you can pin that on Broussard and co who kept on remaking the game out of a petty sense of pride and stubbornness, to the point where nothing they made was up to date (read the Wired article).
So there are plenty of folks (again, not one of them, I never played DN:3D) who would love to see a REAL developer make a Duke Game. They'll excuse DNF for being crap (honestly who thought it could ever have been good? You knew the development history of DNF, how could you have ever entertained the possibility that out of that mess something beautiful would grow?), but they'll buy the next one, hoping that this time, THIS time it will be good.
But if the next Duke Nukem game comes out horrid, then the franchise is sunk for good.