Found this topic at last...I have the same problem as well.
My touchpad on MBP 2016 13" with Touch Bar works fine with all apps, but some months ago the Pinch to Zoom stopped working from time to time. I could fix it by turning the pinching functionality on and off several times in system preference. By it kept happening and it bother me, especially when Im working on a design and zooming in and out is a very often task.
I tried to pin-point the source of this issue and found that Affinity Designer is the reason. My other apps (Adobe PS, AI and other stuff) work just fine. But whenever I launch Affinity Designer, there's a 90% chance that after some time the Pinch to Zoom will stop working. By quitting Affinity Designer, the pinching would work again after some more minutes.
I tried to turn off every touchpad related option in AD but the problem is still there. It's not a big issue, but somewhat inconvenient. Turning the pinching on and off in system preference is by far my only solution whenever this problem occurs, since it always happen when I have loads of design to work on AD and restarting can be a pain in the ...
BTW, I have another MBP which is a 2015 model that comes with a conventional trackpad (instead of a force-touch version), and this problem never occurs.
Could anyone in Affinity dress the issue?