The EEM cables were not hotplugged and I'm not aware of an unwarranted ESD. We've tried a couple of other fixes, swapping IDC cables/SMP wires and reusing working wires, as well as using a variable power supply to check the current draw from the Kasli.
We believe the problem may have occurred because I didn't ground the Kasli/Urukul boards from their floating state. Using a variable power supply we were about to ground the Kasli power connector through the negative terminal, but this didn't resolve the issue.
It's likely the Xilinx chips are damaged. This is doubly suggested from the Digilent software, which doesn't acknowledge the Faulty Urukul boards when connected via the JTAG.