I think the way to do that--and the way I've seen it done in other contexts--is to detect what features can't be saved in the original format and warn the user about about it (with an "I don't care about this" checkbox). I think Word does that when you make a bunch of changes to a document in an older format and are saving it back.
I know users don't read, etc, but the trade you're making is that the simple process of editing a file and saving it is now much more annoying. I just want to make changes to my PNG, not deal with the One True anything.
It's perfectly practical. GIMP did exactly that for years. The 2.8 release notes mention removing the warning now that save and export are separate.
The stated goal was to make it harder (still? I guess people clicked through the warning without reading) to accidentally save in .png or .jpg and lose the layers. But the result, for someone whose usual workflow is to open a .png/.jpg, edit, and save back to .png/.jpg, could not be more user-hostile and obnoxious.
In response to a complaint, someone on the forums wrote:
> This is the way Gimp now works. Of course you can consider this a PITA. But for other folks, losing work because they saved as JPG instead of XCF is also a PITA. The philosophy is that people that are impacted negatively by this change are people with very simple work-flows who would be better off using simpler software (XnView, Digikam, Lighttable...)
In other words, all of you people with simple workflows, that worked just fine in Gimp for years? Now you have to go off and learn some new software, because Gimp is for Serious Graphic Design™ only. Ugh.
I got excited researching this because I found a changelog for Gimp 2.8.4 that mentions patching the behavior to be sane, but then I realized that's only a patch in the unofficial OS X build. On Linux, the same nonsense in the latest version.
The existence of several counterexamples of it done would seem to disagree with your point about it being "impractical". Paint.NET warns it'll have to flatten layers when saving as PNG, Notepad will warn if you try to save Unicode-laden text to an ANSI .txt... not to mention several blanket warning systems...