Krita seems to save everything if auto-save is ON. even hidden and not-edited paint layers. By 20 layers I need to wait several seconds every time auto-save kicks in. No blame to auto-save, I love that feature. It drains also lot of performance meanwhile I paint in Krita's last public release. For work I prefer without doubt 3.1.1
With Krita 4.0, saving happens in the background, so you shouldn't have to be waiting to keep working. Can you try out the Beta and see if it still has issues? https://krita.org/en/item/krita-4-0-beta-1/
As Scott said, in 4.0 Krita saves in the background, so this is fixed. And in general, it is impossible to only save changed layers -- zip files don't work like that. You can save the entire file, but not change parts of it.
@ Scott Sure. it's a honor to check out your builds. Love your work!! Currently I cannot buy I wanna donate later on @ Boudewijn I posted this report also because I remembered years ago when blender.Org foundation introduced sculpting, they saved sculpt edits in a separate file. Now Krita needs not as the file size blows not up like with 3d but nevertheless the technique pet see is interesting - for the auto save feature.