Glad to hear that you were able to save your work.
Basically, all files that you save in ATG are .at2 files. They all act like a game or a scenario, but some are intended to be a template for games. For example, the random game generator. So, the file "anewdawn-3.at2" acts more as a template to generate games, or, as an alternative, the core for game or scenario. All of them can be stand alone, but some, like the aforementioned "anewdawn-3.at2", aren't meant to be played. They are meant to be the core to a game. For that, the masterfile is loaded and is attached to the file. When a masterfile is attached, you can only edit things on the map, units, and place them on the map. Most of data for SFTypes, terrain, LOCTypes, etc., can't be edited unless you remove the masterfile. But, if you edit the masterfile, say change the combat strength of Medium Tank II, it will automatically be carried into all scenarios that have that masterfile. That way, you don't have to edit every game, just the core. You can also load a masterfile at anytime, but beware that it will overwrite all the data that are in the slots that are in the masterfile. So, if your file has more terrains than the masterfile you load, you will keep all the terrains that are above the ones in the masterfile, but all the rest will be overwritten. The same is true for events.