I did a quick test, the best way, I think is to take the 3d comic image into clip studio or photoshop, pump up the contrast a little bit and then convert the image to black and white - what you'll get is the blue will probably drop out and the right will then darken to black, this should leave you with the image you'd see in the red eye (which, iirc is your right).
(I tried this on a Mark Bagley spider-man image I found online and it actually works surprisingly well)
You'll have to play with contrasts to get exact results, and the bigger the image the better - you're basically looking to make one colour much darker than the other and then to make the lighter colour just vanish. Any overlap will be black (or at least dark) so you shouldn't lose anything important.
You won't get a true centered image (ie one that combines both left and right) but I can just can't figure out a how to do that in a couple of easy steps (or even hundreds of horrible complex ones, someone smarter than me may have figured it out) (Google search is a bit useless, did find one website that promises to recombine left/right images but it's mainly for colour photography and I couldn't get any results from it at all, and it's mostly in russian)
