In Fallout 3, bugs are still prevalent, and sometimes named non-player characters in Fallout 3 can disappear or die by themselves. Walter and Billy from Megaton standing in some uncharted void below Springvale. Once you debugged your game, save it, and put it back it the original Xbox 360 file then in your Xbox 360 and everything will work as if it was the first time. Everything will work exactly like when you play Fallout 3 on Windows so you don't have to worry about anything.
Note that you can convert your Xbox 360 Fallout 3 savedata for the personal computer version with Modio: extract your Xbox 360 savedata on Windows, extract the file within the Xbox 360 savedata on the directory Fallout 3 uses for saved games then play it on Windows. This article talks about using console commands to compensate for bugs and, as such, only applies to the PC version, with the exception of the specific part concerning consoles and the 'Getting Them Home' section.
