If you are using Microsoft Word it is very easy to scramble your novel in a way that will not affect its word count.
The procedure for Open Office is essentially the same, except that Open Office refers to 'Regular Expressions' instead of 'Wildcards'. (Thanks to Peter Dudley for this advice!)
You can get the same effect in a more cumbersome way by just doing a find-and-replace on every letter in the alphabet, one letter at a time. Open the find-and-replace interface on your word processing program and tell it to replace every "b" in your story with an "a," and every "c" with an "a," then every "d" with an "a." And so on.