I wish I read the manga and finished it. I feel Hiro Mashima and his staff didn't explain the full extent of his sword. Runesave cuts intangible and not the tangible. Intangible can be argued and extrapolated to many things: magic (the most common energy in Rave Master), mind (which we saw in his fight with Let), and then for battle threads, it can be a messy slippery slope.
I can be wrong. Maybe, it's just a temporary sealing of the Chakra and not a permanent seal. He couldn't do that to Elie's Etherion. There has to be some limit to powers.