I am not sure what you want to change but to change login.js you can goto project folder>>deployment>>web and then copy the js folder (this will include 'login.js' and 'login_i18n.js') then goto project folder>>theme and paste the js folder in theme folder. Then you can make any change you want o lgoin.js and deploy your application which will copy the chagnes made to login.js to the deployment folder as well.
Hope this helps!
Are you using a custom theme? Because then you should make these files in your custom theme.