申請して返事が来る前に帰っちゃった場合ですが、何の問題もありません。このことはApplying to Change Terms and conditions or Extend Your Stay in CanadaのP7にしっかり書いてあります。下記参照
Q. May you leave Canada before your request for an extension has been finalized?
A. Yes you can leave Canada before your extension has been finalized, but if you leave temporarily and do not have a valid Student or Employment Authorization, you may not be able to come back. It is your responsibility to make sure that your request for an extension has been approved. Otherwise, you will have to apply at a visa office for a new Student or Employment Authorization and pay another processing fee.