I migrated to the "New Freshbooks" almost two years back, I think -- and for the most part it went fairly smooth. The design is a little cleaner, although there are a few features of the old system that aren't present.

Initially, when finding a feature gap, I assumed it was coming. Some of those features, however, still haven't come, and I'm tired of waiting. In particular, the ability to add taxes automatically to all the lines of an invoice is a real thorn in my side because for some of my clients I have very detailed timesheet invoices.

On the latest example of this, I had 87 lines. Going through 87 lines one by one and clicking "Add Taxes", then a checkbox, then save is ... repetitive, boring, and just the sort of work that computers are great at and humans are less great at. And yet I've done this on a whole ton of invoices because there wasn't an automatic way to do this on the new FreshBooks.

But no more. I gave up waiting for FreshBooks to do it and wrote a little piece of JavaScript that I can run with Tampermonkey:

// ==UserScript==
// @name         Add HST to FreshBooks Invoice
// @namespace    http://codiform.com
// @version      1.0
// @description  Go through a FreshBooks Invoice and add HST to each line
// @author       Geoffrey Wiseman
// @match        https://my.freshbooks.com/*
// @grant        none
// @run-at       context-menu
// ==/UserScript==

(function() {
    'use strict';

    let popovers = document.querySelectorAll("div.js-tax-picker-popover");
    for( var popover of popovers ) {
        let hst = popover.querySelectorAll("td.js-taxes-popover-checkbox")[1];
        hst.querySelector("input").click();

        popover.querySelector("button.button-primary").click();
    }

    alert( "Done adding HST to Invoice." );
})();

Now I just edit an invoice, right click, select "Tamper Monkey" and then "Add HST to FreshBooks Invoice" and wait for it to run. Way, way better than three clicks per line.

If you have the same problem, feel free to adopt my solution. You might need to adjust the index of the popover checkbox if you don't want to add the second-defined tax (I used to have PST and GST), now I just have HST -- but other than that it should probably work for you.