I agree as well. Removing the solids will help water quality, but it won't replace the minerals and such that help provide stability for the system (pH, KH, ect), nor will it impact the dissolved wastes. Those only happen with removal and replacement of water volume.
If you are having problem cleaning the full substrate in one go, I would advise cleaning more often to reduce the build up of wastes, or to do two water changes--ie, vaccum, add water, vaccum again, add water. Won't hurt the fish, and will be better in the long run than inadequate cleaning or insufficient volume replacement.