I do all non long form drafting in Obsidian in one note and noodle with all the links and outlines until it is worthy of editing and revision.
At that point I copy the draft content to Scrivener (I get too distracted in Obsidian).
If the content goes out the door I save it in Scrivener to PDF (images and all) then put that into obsidian. Both the draft and the final manuscript are named the same but with a “- draft” or “- manuscript” suffix. In my process a final draft and a submitted manuscript are artifacts.
I resisted (early on) the use of many folders; sorta defeats the purpose of linked thinking. If you use links it makes no sense to duplicate notes in separate project folders. I know I sound like a broken record … If you title your notes appropriately, Obsidian search is the only organizational friend you need; and perhaps patience.