Normally you can't do it. If you need to save modified data, you save it in Local Storage. So on start of the game check Local Storage, and if it has any data, load from there, otherwise load the file included in the project.
There are some exceptions - if the game is hosted on a web server, you can use a php script to overwrite json file. In NSWJ export you also may be able to update it, if the user has write permission to this folder.