I totally agree that working in layers is fantastic! However, from my experience it seems that you have to be especially careful that you're pixelling on the correct layer....I use layers mainly when it comes to opacity, but otherwise I haven't broken out of the habit of saving multiple copies of my work as I go along just in case I need to backtrack for what ever reason.

The isometric thing is adorable btw and I hope you do more with it o w o Isometric pixel art can be pretty challenging, especially when you mix non-isometric elements into it.

And I also follow the layer process when it comes to sketching and fleshing out a piece, usually. For anything that's around 50x50 pixels big and lower, though, I tend to just have my refined lines and sketch on the same level.

Keep on making r/pixelart a better place ;D