As I said, you'll have to recompile / publish the .fla file(s). Open the megazine.fla in the Flash IDE and publish ist (Ctrl+Return). If it's something affecting the interface (e.g. LibrarySWF.as) open the interface.fla, same procedure.
Sizes in fullscreen are the same as in normal mode, unless you use liquid scaling. This is still not quite usable, though (as the GUI scales, too). So alternatively you could have a look at the Main.as, specifically the onFullscreen function, and make the changes you need in there.