My site uses server-side includes. If I switch between the Code tab and the Visual Editor tab, the page loses its ability to include after I upload it to the server. Any suggestions?

This might sound obvious, but it has never been a good thing to switch between code editor and Visual Editor. I think there is even a warning that it will change the code and asks if you want to save your files before making the changes. Use one, or the other, but not both(on the same file). Your files will be changed by switching back and forth, and it may affect other things besides the "includes" and really mess up your work.