Oh no! I am sorry to hear about your Jrks. I suspect the biggest thing you can do to limit these voltage spikes is reduce the Jrk’s max acceleration and deceleration, plus its hardware current limits.
As for other things you can do, shorter power leads and additional capacitors would probably help. (Ferrite beads and twisting wires are more effective for reducing high frequency noise like EMI.) Using something like one of our shunt regulators might also help; the 26.4V, 2.80Ω, 15W model (item #3775) would probably be the most appropriate one we have for your application. Please keep in mind though, our shunt regulators are only designed for clamping occasional short (up to tens of ms) pulses. If you decide to try one, I strongly recommend looking at the spikes your system is experiencing with an oscilloscope first so you can see how high and long they are. I suggest doing these tests with a lower supply voltage to avoid damaging more units.