Hello there. Some weeks ago I've started to work on something with Fallout 3's G.E.C.K but when I was back in the normal game (without any mods or anything changed/altered), it could load mysavegame but told me that some elements where missing and they will be removed when the save will be loaded. I don't like something like this to show up, so i'd like to make a backup of all the files changed by the G.E.C.K. I made a backup of Fallout 3's .esm and was thinking it was enough to not get this message again but i was wrong as it stills show up. So here's my question, what are the files that are changed automatically by the G.E.C.K for me to replace them when i'm playing and not in the level editor to not have to risk to loose/alter something in my own savegame ?

The optimum solutioon would to be able to install Fallout 3 twice, but it seems impossible to do it (one install to play, one to edit everything).

The Save contains references to mods and any elements in them, which were active when it was made.
When loaded with out those mods present, it pops that message.

Saving after loading this way "cleans the savegame" if references to the missing mods and things based on them.

About the only mods which will not allow a save to load without them would be race mods if the player is of a custom non vanilla race.
Switch them back to vanilla and then remove the mod in this case.

No master files get altered by anything you do in the G.E.C.K.
All these "changes" are saved as part of your mod.

Thank you for the answer Michele.

I see, this explains why fallout3.esm has the exact size before and after editing.

So if I continue my work and can create anything I want, there is still zero chances than in the future something won't be able to load or won't load corectly then. If so that is good to know