I know for a fact that the Additional Ammo mod overwrites the basic.cfg file, and it's not the only mod that does this. As noted above, when a file is overwritten by a mod enabled with JSGME, the ENTIRE file is overwritten, not just the few lines or blocks of data used by that mod. Whatever previous version of the file you were using, including any edits made manually by you or by previously enabled mods, is gone until you restore it by disabling the mod that overwrote it.
If you manually edit your basic.cfg file, then enable Additional Ammo using JSGME, you will lose whatever manual edits you made because the basic.cfg file you edited has been completely replaced by the one from Addl Ammo, which is the original GWX basic.cfg with only the changes needed to provide you with more ammo.
If you then enable another mod that includes its own version of the basic.cfg, you will lose your additional ammo because the version of the basic.cfg that included it has now been overwritten and the newer mod's version of that file doesn't include the edits for additional ammo.
My SOP is to do all edits to the basic.cfg manually to avoid this problem. Bottom line is, if you enable a mod with JSGME and get a message saying that it's overwriting a file that another mod already changed, or that you yourself changed, then if you proceed you will risk losing whatever changes the previous mod made to your game AND may be taking out stuff that another mod needed to work properly, leading to potential CTDs and other problems.
If you get one of those messages it's always better to stop and investigate the possible conflict, or ask here about it, unless you already know that you are not making changes with one mod that will undo something you need and want to keep from another one.
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