Can I scramble my novel before submitting it to your untrustworthy word-counting goons?
If you are using Microsoft Word it is very easy to scramble your novel in a way that will not affect its word count.
Open the file and make a new copy of your novel using 'Save As...'
Open the Find and Replace dialog box (Edit -> Replace).
Click the "More" button to expand the box.
Check the "Use Wildcards" checkbox.
In the "Find What" field, put this: [a-zA-Z0-9] (include the square brackets, no spaces before or after)
In the "Replace With" field, put this: a
Click "Replace All"
Save the scrambled file as a text file, and upload away!
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.