My larger eel shakes his head when he's searching for food, such as when he takes a snap or two at the puffer (puffer always tries to steal the eel's food), he takes a couple of snaps at the puffer, and then shakes his head back and forth looking for the puffer and his food. Eels have pretty poor eyesight, my eel has to have his food basically bounce off his face to see it right. So your eel may have been frantically searching for your damsel or something, maybe he was trying to nip him, maybe the damsel was nipping at the eel (if the damsel is large this may be the case, I've heard horror stories about aggressive and fearless damsels).
Dunno about the "scratching".
So long as the eel is fine then don't worry too much. Just keep an eye on the two of them and see how they interact, only thing you can do now is observe and try to see a pattern.
