I use Paint.Net a lot to create images for Word. So I save in .jpg org .png. And everytime I save my work (which contains layers), Paint.Net asks if I want to flatten it.
Can you please add an "Remeber my selection" check-box, or auto-flatten the image. I think, after seeing that dialog-box for 100x times, you know that there will be no layers afterwards.
Alternatively, you could add a command "Save As Copy..." which doesn't ask for flattening, and will not change the currently active image. (This solution would not require you internally keep track of the user choices.)
Thanks!