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If these sites were then interlinked, would I be ok on the basis of interlinking between separate IPs, or will it be penliased?
When the IP header gets stripped off, you are dealing with layer 2 frames and not IP packets, so even if your host has more than 1 IP address who cares? Thats the nature of VLANS the wire speed switching technology deployed world wide.
Conclusion - your safe;)