Very strange one this.
So I needed to touch up some frames of an animation, so I did so in Affinity Photo which wasn't what was used to render the original PNGs.

If I go to Import, select frame one as seen below.

I end up with this, any of the frames I edited in Affinity Photo are invisible.

There is a work around however, as long as frame one was edited in Affinity Photo, all frames (the ones edited with Affinity Photo and the still unedited) will be visible like normal.
So very strange, but at least there is an easy enough workaround.