I had my hinges repaired with my runcore in, no problem. I took it in to the genius bar, they looked it, checked it in for hinge repair, as they were doing this, i mentioned the runcore and they said "no problem". About 6 days later it still wasn't ready (around iPhone 4 release, delays) and i was leaving on a trip, so i had them convert it to a depot repair and send it out. I asked again about the runcore at the depot and he said the only reason they would mess with it was if the found a fault. So i sent it out and got it back a few days later as good as new with my runcore still there.
I had the hinges repaired on my MBA 'A' at the Houston facility with my Runcore 128GB inside. Not an issue. Just for protection, be sure to backup your data and keep a hardware listing.
BTW, I shipped out my MBA late on a Wednesday and had it back in my hands early AM on that Friday. (Even so, it was a painful Thursday without Air...!!)