I have adjusted wait list through CM. I have been told that it did not put us further down the list (It probably depends on what kind of change).
I am far from an expert on this but I would not just let your existing waitlist ride and adjust afterwards. If you are borrowing points, have already borrowed some and have others back in the use year I would think it could really mess with your points not to mention if you have waitlist active to 7 days. With all that said I would definitely call an not do on-line.