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So what I'll do now is skip the LVDS on the FPGA and simply use LVTTL to/from the buffers.
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A much more safe solution, I think.
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Part of this can be solved (in my case) by instructing the installer not to powerup the main unit until the remote unit has been plugged in.
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Simply consider that people (and particularly hasty service guys) use to hot-plug any connector, that you won't even think of. Unfortunately, they don't confess, just return a device "defective on arrival". It can be really reassuring to make the device hot-plug capable, if ever possible.
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