New Technology for separating close boiling points?

Have you considered pressurizing the container to raise the boiling point and increase the spread between the two isomers?

Do the two isomers absorb at different wavelengths? You can flash radiate with one wavelength specific to the lower boiling point isomer.

Can they be crystallized? Crystallization after distillation or some combination of both would separate them in short order. You could potentially use what @LuckyGuy mentioned and use a spectral method to separate the crystals.

Can you pressurize the liquid, Carbon Dioxide has different points of boiling and solidification under pressure ? ?