Just a guess... some adjustments (layers) look a little different at anything less that 100% view. When you flatten while viewing at, say, 33%, the display might appear to change.
So as a test, set your view to 100%, then flatten, and see if you notice any change.
BINGO!!
I tried your suggestion and when flattening at 50% viewing or greater, no changes in screen appearance occur. At less than that, changes begin and at 12.5 % viewing the changes were greatest. My image was 20x28 so viewing at this small size was needed to get it on my screen.
Thanks for the suggestion!!
MDIJB