Is my COE needed after I use it when I land in Japan?

I've recently had to make a sudden schedule change for my classes, and had to switch from the April term to the July term. My COE becomes invalid May 15th, because it was issued for my April term. My question is, If I land in Tokyo before May 15th, can I use my COE to get my visa then? And then just extend the visa as necessary? I've asked my Language school about this, and I don't think I'm getting across to them. If you have any advice it's much appreciated!