In the questioning of David Boies, Judge Smith (the lone Republican appointee on the panel), asked him whether the failure to defend Prop 8 was a "nullification" of the efforts of the proponents and the choice of the voters in a way that was akin to a "veto" by the elected state leaders. Of course, a veto of an initiative is not allowed under the Constitution. So, conflict? (Here's where I'm hearing an ominous duh-duh-duh in my head.)
Well, not really. Boies points out that the California Supreme Court was in fact asked whether Brown and/or Schwarzenegger were legally obligated to defend Prop 8. And, in fact they were asked by the "Pacific Justice Institute" exactly that question. PJI was first denied by the the 3rd District, and later by the California Supreme Court.
There is a process for appellate courts to ask state courts a question about state law, called certification. Basically, they "certify" a question, and the state supreme court can answer it. It would delay the process substantially, and given the quick dismissal of the PJI attempt to get Brown to appeal, doesn't really seem either necessary or worthwhile. Essentially, the state supreme court has spoken on this issue by failing to force the appeal.
However, if the panel really felt strongly on this subject, they could go to the State Supreme Court. We would probably hear about that fairly soon. But, really, don't expect that.