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The measuring was done of course with no power using a DVM.
Replacing the Altera component usually solves the issue, but we still don't understand the behavior because the phenomena repeats on different boards and on different LVDS lines
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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?