There is no supported way to update the include files like this. However since included files are referenced with standard include and require once statements you could change the locations of the files so long as you make sure you update any of the include file statements that reference that file. This is not something I would suggest though as it will likely be more trouble than it is worth. On the upside since it is server side code that is in the includes you do not have to worry so much about users visiting the page directly or anything like that.