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If replacing the FPGA fixes the low impedance pin then you must be causing damage to the pins. I'm always very wary of connecting FPGAs on different boards directly, or exposing any FPGA pins directly to external connectors for that matter. I'm assuming these two boards are not in the same chassis with the same power supplies and ground planes? Depending on the setup between the boards you could easily get an inadvertent over-voltage situation on those lines.
Can you give more information about the physical setup between the boards?
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The two boards are not on the same chassis but one of the boards is supplying power to the other, such that the power and ground levels should be the same.
Regarding the damage, in one of the cases we have replaced the FPGA and noticed that the FPGA that was removed is still having these low impedance pins.
Thanks,
Ilan.