How to regen a DC motor from the high-side of a boost converter?
Hooray, I don't need to add any circuitry! As it turns out, the DC-DC controller chip I am using, the LTC3787, actually has internal logic to dump the high-side caps to the low-side through the inductor when the output voltage is 10% higher than the target. 

This is not mentioned anywhere in the datasheet, except if you look very closely at the block diagram, and notice there is an extra comparator connected to the Feedback pin which triggers the top MOSFET. I only discovered this behavior by simulating in LTSpice to see what would happen when output voltage spiked.