The mod system normally reverts all script files back to the original version before applying any mods. In the case of Aric's mod, the "backup "folder is deleted to create a new reset point for the script files. Any changes made to the base game before replacing files for the mod would be replaced by the file replacement. Any changes made to the base game after a new backup has been generated but before the mod has been applied in-game will erased. So long as you do not use the mod system after applying the mod, any changes you make to the base game will be safe from being erased or overwritten.
Any changes to the scripts in "Put in Strive Game Files" are not guaranteed to appear in the final code, as the mod may overwrite the code when applied. Any changes to the mod's scripts outside of the "IMPORTANT - READ THIS BEFORE INSTALLING" folder will only effect the game if you made the changes before applying the mod, as most files (excluding those in "scripts/aricsexpansion" folder path) are ignored afterwards.