The only way you could remove or alter the vocals would be if they are in the exact center of the stereo image and don't have a lot of chorusing, reverb, or other effects on them.

The software that removes does so by reversingthe phase of one channel of the stereo image. What happens is that the reversed phase cancels out anything in the exact center of the image (usually vocals, sometimes lead guitar solo)

Of course, if you have a Dolby 5.1 image to work with, it's a little different... most of the time the vocals are in the front center channel, so you could pull that channel out entirely and reduce the remaining channels to stereo.

Hope that helps.