gistfile1.txt

User.find({'profile.picture': /twimg.*_normal/}, function (err, users) {
    if (err) { debug('Username err: ', err); return next(err); }
    for (var i = 0; i < users.length; i++) {
        user = users[i];
        if (user.profile.picture) {
            user.profile.picture = user.profile.picture.replace('_normal', '');
            user.save(function(err) {
                if (err) { return next(err); }
                console.log(user.profile.picture);
                done(err, user);
            });
        }
    }
    process.exit(0);
});

and the process.exit is being called before any of the save methods can complete. It should be added as the last task in an async series

https://github.com/caolan/async#each each(arr, iterator, callback) where arr is the users array, iterator is where you call the save method, can callback is where you call process.exit(0)