Now of course, Duke has neither one going for it as there is virtually no substantial fan presence for Duke football. Most Duke basketball fans across the country are not alumni and do not have direct connections to the university. Even among the ones who do, not all of them root for Duke football. Many if not most Duke fans have a college football team not named Duke that they root for if they are interested in college football at all. Of course, the people on this board, and the people not on this board that they engage in Duke fandom mostly fall in the minority in this regard. With that said, there are certainly scenarios in which Duke gets left behind. Most if not all of these scenarios involve UNC jumping ship to the SEC, and the remaining Big East football teams are stronger than the remaining ACC teams such that the Big East hand picks which ACC teams to invite instead of the reverse.
Even in this worst case scenario, what I see as the likely outcome is that of the 67 or 68 current BCS teams (counting TCU and depending on whether or not ND remains independent through all of this), only 3-4 will be left out. Even with the info I laid out above, I don't see Duke as one of those. For this scenario to play out, the Big East has to be left mostly alone by the SEC and Big Ten. Let's say that the Pac-12 adds Texas, TTech, OU, and OKST. The Big Ten could plausibly add ND, BC, Kansas, and Maryland (if they tried as hard as possible to stay away from the Big East). The SEC adds TA&M, UNC, Va Tech and Missouri. There might be more realistic teams out there, but again, I was sparing the Big East for a worst case scenario, and the SEC doesn't want to expand within it's footprint or double up on a market. Out of the Big 12, Iowa St, Kansas St, and Baylor are out in the cold already. Let's swap KState for BC because Kansas fought really hard for them, though it not like Kansas would be at the top of the Big Ten's list in reality, but for arguments sake. Even going way out on a limb, I just can't see Iowa St or Baylor getting a Big 10 or SEC invite and I don't see them above Duke on the Big East's list. That's already 2 of the 4 teams.
The Big East survives with it's current 8 plus TCU coming in, so they want to add 7 more and are left with 9 ACC Teams to choose from (UNC, Va Tech, and MD are gone). As long as there isn't a death penalty issue with Miami or lingering spite, the two former Big East teams (BC and Miami) get invited back. That leaves 7 for 5 spots. Florida State is almost a no brainer with it's current status and past history in football. Georgia Tech adds a top ten market and is a shoein. NC state has the biggest local fan base left in NC and would offer a big chunch of the Raleigh market and a small chunck of the Charlotte market. This leaves 4 (Clemson, Duke, UVA, Wake) for 2 spots. All four are either in a bad TV market, or in an already accessed market, so we compare potential match-ups that they bring. Despite falling on their faces compared to expectations most years, Clemson does recruit well and have potential. UVA is up and down, and despite being mostly down lately, they are at least not in a used market and are up sometimes, so Duke and Wake are left out. If one little thing changes in all of that, I see no way that Wake goes before Duke, so we'd be back in.
Even if all of this doomsday stuff played out, I would see Duke joining up with the 7 non-football Big East teams (Nova, GTown, Marquette, St. Johns, Providence, Seton Hall, and DePaul) along with a few others (Memphis perhaps) to form a non-football conference. Duke could then play Army/Navy style independent football as well in whatever form of football is left for those not in the super 64. If those 9 aren't enough, you could look to poach top mid majors in the area (Temple, Xavier, etc.) to round out the conference.
The true doomsday scenario beyond this is if the stars align to leave Duke out of the 64 and then the 64 split from the NCAA. This would keep Duke from even being allowed to participate in a nationally relevent basketball championship event. We'd be relegated to the basketball equivalent of the FCS championship. Throwing the factors necessary for the super 64 to split off in all sports and not jut football to the factors needed to keep Duke out of the 64 makes this an extreme improbablity whose odds are around the same as Duke football suddenly winning a National Title.