I am not really knowing PHP, but I try to understand Expression Web. And maybe this gives you a clue, although it won't really help, if you want to work on your site on line:
I understand that you are trying to update the 3 files while working on a website that is located on a server, running FPExtensions? Now I learned that in Expression Web, you cannot use any Dynamic Web Template features (all menus blanked out), while working on a website that runs on a server with FP Extensions. It may be for the same reason that updating files from a DWT is not possible...
So you might have to (re)design your site locally (hard disk based) and after that publish it to the server again.
I can recommend the book "Using Expression Web" by Jim Cheshire where a lot of "Trouble Shooting" items are listed. This is one of them.
Wish you a lot of success / Succes gewenst,
Bert