Fixed. Nothing changed in terms of how to do it. The appropriate warnings are on the blog post. I found that having the Encode HTML Entities checkbox checked breaks the patch.
So far it is working great. Right after I saw your post, I was looking at an editor instance that didn't work like my previous test. That instance had Encode HTML Entities checked. I didn't know why it didn't work at first.
I tried to patch around it with custom tags like <BODYPREPENDBEGIN /> but that didn't work either.
The way it works, comments are inserted before and after the prepend and append and everything between them as well as the comments are removed on save. If the comment tags are altered, the search and replace does not work. I'm still not sure why CKEditor seemed to leave the outer comment tags alone, but messed up the inner tags, at least that is what it looked like was happening.
