I code my websites by hand, so am not very familiar with WYSIWIG programs. A friend of mine recently made a website using iWeb and there were a few issues with it so I made a few changes to the code ... I replaced the image- and script- heavy navigation bar that didn't work in IE with a simple html/css one so it would work in all the browsers, and reduced duplication by removing a large background image that was common to all the individual page folders that iWeb produced, placed one copy in an images folder and redirected the pathname on all the pages to that folder. Other than that, I did not touch the folder structure set up by iWeb.
My question: would my friend still be able to download the files, make changes to the website in iWeb and re-upload them despite the changes that I made?
They should be able too... however there's no guarantees that iWeb won't reintroduce those errors back into the source code. Welcome to the world of WYSIWYG editors, where people can patch together a website design without ever having to know a single element (and thus break everything without knowing)