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The whole hardware design approach here is not going to work :)
First thing that you'll experience is sporadic remote FPGA reconfigurations due to noise pickup on 100 m nCONFIG line.
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This is likely, even if nCONFIG is a dedicated LVDS twisted pair?
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As to ESD then "human body model" is just one of the several ESD model. There is a "machine model" and most important for you - "cable discharge model" (
http://www.national.com/an/an/an-1511.pdf). They differ greatly in the ESD power they can apply to you circuit (e.g 15kV "human" is not equivalent to 15 kV "cable").
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I realise(d) that already, however, AFAICS the ESD specs for buffers seem to increase for both values when the human body model value increases. I figured, that the best I could do, was find a buffer IC that has the highest values for the human body model, and that will automatically make it the most robust for the machine model (albeit with lower absolute values than for the human body model). And considering that, the best buffer ICs I could find offer 15kV human body model of ESD protection, which translates into a lot less in the machine model, but since they're the best I can find, what else can I do? Hmmm, I see that the reference you provided outlines some of the other protective measures I can take. Interesting read, thanks.
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You'd need a reliable way to configure remote FPGA. You might add a small flash-based micricontroller on the remote side with LVDS-to-LVTTL buffers, send FPGA configuration data to MCU over LVDS with some CRC. And then MCU configures FPGA.
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If a 100m LVDS driven nCONFIG twisted pair is going to be prone to occasional transients which are going to cause it to misread as a spurious undesired low level, then the most likely alternative is that I use a flashrom for FGPAremote as well, and then program the flashrom from inside the FPGAremote if I need to adjust the programming/logic (yes, I know that makes me vulnerable to powerloss during reprogramming, but that is an acceptable risk).