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The two boards are not on the same chassis
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How long is the cable between these and what sort of cable is it? Is it shielded? Does it allow for a very low impedance ground path between the boards?
I'm concerned the topology of your system is causing the issue. If you've removed a device and that device still exhibits a low impedance path from a signal pin to ground then it's damaged. A poorly considered interconnect cable between the boards could be the cause.
If connecting any 'significant distance' (a bit vague, I know) you need to consider isolating the connection. There are many contributory factors as to what constitutes any significant distance, but the questions I first asked are all relevant. On top of that will be the signalling standard you're using. You also mention supplying power from one board to the other. How good is that PSU? Is it sufficiently decoupled at the far end? If it's powering your receiving FPGA then I hope it's doing it indirectly - i.e. via another regulator(s) local to that FPGA.
Cheers,
Alex