Yeah the FPGA and even the FX3 are fully loaded from the host. There is
nothing permanent written on the B2xx devices, so worst case you unplug /
replug and it will reprogram everything starting from the FX3 ROM loader
which you can't possible overwrite.
As for FPGA mods, as long as you don't change the UCF/Pin Assignments, then
it would be pretty hard to cause any damage to the board that a reboot
wouldn't fix.
Cheers,
Sylvain
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