I know this is a really old thread, but this is possible. I landed here after googling how to do this and figured it out. I'm using Affinity Designer though and haven't tried this in Photo, but it is hopefully the same in both. So, for anyone who lands here...
Click on the layer that you need to edit and need to be "unlinked." Then with the selection tool selected, in the top bar there should be a button that says Replace Document.
If you click on that, and replace the document that way rather than through copy paste, it breaks the link, so to speak. Though, you will have to do this every time you need to make this edit. Anyway, now you can edit each instance of the document without editing them all at once.