Yes, if you cut a song up and remove vocals in just part of a song there will be a noticable difference in music quality and/or volumes. I tried this sometime ago and with the particular song I was working with I did not like the results. Too unprofessional sounding. Although every song is going to be different so it might be worth a try. If you have good wav editing software and know how to use it you might be able to create something satifactory.
Wally