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The two boards do share a common chassis, but their operating voltages and grounds are generated by separate isolated DC/DC converters. Their grounds are definitely close enough to not require AC coupling on the transmission lines.
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A problem may arise, when the LVDS signal ground is the only ground connection between the two systems or even the only existing ground connection at all. Then high intereference currents are
attracted by this connection. An additional ground connection and a common mode choke including all data lines and the signal ground (e. g. a ferrite core around the cable) may be advisable.
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