Parsing a CSV file in node.js and express.js
Your code is fine and the approach will work. However, I do have the following comments based on my own experience.


In the case of error response, why not use the error object to capture the error details and pass return next(err), something to the effect of: 

//handling errors in your code woud look like
if(somethingisntright()){

    err.message = 'Something is wrong';
   next(err);
}

//error handler presumably in your app.js
app.use(function(err, req, res){
//if you have multiple errors you could articulate based on assigning err.status
    res.json({
        status: 'error'
        message: err.message,
    });
});


This will reduce the amount of error handling code in the current module and centralize error handling thus reducing maintenance effort in the future.
I'm not sure if it is worth it but you may want to consider short circuiting your logic so that the code handling line numbers >= 3 are handled first. It saves some cycles having to evaluate the first two scenarios for every other line regardless.