AFAIK white box emulation has been around forever. I'd be surprised if it isn't already worked out in the courts, since this has been happening since before computers were around.
I don't think Intel wants to waste resources (and get bad PR) if it isn't a significant threat to their bottom line. Microsoft saying they are going to emulate x86 on ARM with low overhead (and thus making it possible to switch to ARM and still use tons of legacy software) is a much bigger danger to them.
Isn't there some notion that you have to actively defend a patent to enforce it? That is, something where selective enforcement puts you in a weaker legal position?
Edit: The legal term appears to be "the doctrine of latches"
QEMU emulates X86 chips as does other emulators. I wonder how those are effected?