Internal LVDS for between-board communicatino

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I don't claim to know your system enviroment in detail, but a LVDS connection without a acompanying signal ground has a high risc of catching interferences, with or without AC coupling. Also possible damage to the FPGA IOs must be feared.

You have to consider also higher frequecy interferences, not only DC and mains frequency potential differences. Would be different when using a transformer coupling, e. g. by ethernet magnetics. But this also requires 8b/10b, as suggested.

Another (DC capable) solution is to use digital isolators from NVE or Analog.

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Thanks for all the help :)