Sorry, I should have included more detail - this is for a custom FileType plugin which loads the image just fine, it's when attempting to save I'm having trouble.
I set the pixel like this:
layer.Surface[x_pos, y_pos] = ColorBgra.Transparent;
Which both displays and 'eye drops' correctly.
if (scratchSurface[x, y].A == 0)
This just returns 255, despite PDN clearly showing and displaying A=0
I'm also iterating through multiple layers so not sure if this is the right way to do so?
foreach (Layer layer in input.Layers)