I didn’t specify a program to use, but I did not know this. A step in my personal workflow I neglected to state is to flatten all layers but I’m not sure what the best way is, so I’ll just say I am open to ideas for better ways.

There should be a test suite for image editing applications which will validate the different ways of editing a file to see which ones work as expected and which do not. I’m thinking something similar to web standards test for browsers. Does something like this already exist?