Flattened and Cloned, Edits Not Saved

I flattened an image and made a duplicate layer to clone on, which I was able to do. Though after flattening are layers really possible? Then I did some more cloning without making  a duplicate layer. When I saved the image-- I also get the Replace option becase I'm updating old edits--the old image is saved and not to one with my new edits. I did notice when working on the image there ws aother image layer peeking out from under it. Is it possible for me to save my latest image with its clones or do I have to start over?

It sounds to me that you are saving a lot of picture files which are really work-in-progress. Why save all these and fill up your drive with suboptimal pictures?
If you save the file in the native format, you can preserve the layer structure, reopen subsequently for additional edits.

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