I've been thinking about it, and it can be done, but it would take a lot of work and be a PITA. But I thought I would bring up the thoughts anyways. You would need two JB3's (which I don't have, but I know a lot of people do).
Thus far, we know that the JB3 will take a 96k signal. The file header is written wrong, that needs to be changed, but apparently that's easy. The problem is, is that 96k is too fast for the JB3 processor, so it results in glitches and dropouts. Now I'm going to go on the theory that lightning never strikes the same place twice. So, if you were recording with two JB3's at the same time with the same signal (optical splitter), then both recordings would end up with random dropouts, but not in the same place. Here's where the hard work comes in--you would need to load both files into some sort of wav editor where you can do two tracks of stereo at the same time, and be able to line the files up against each other (I can do it in Samplitude). You would then have to painstakingly go through and take all of the good parts and throw away the bad parts, save them as one file, then there you go! A clean 96k recording.
Food for thought.