It sounds cooler to say “Refactor.”
What I’ve done in ulysses in the past is to import a long sheet of Kindle Notes from a book. Working down the page, I’d process the literature notes into permanent notes. Then, once all the notes were processed (or deleted), it was easy to move through the sheet, hitting the hotkey to split the sheet into separate files, or … atomic notes.
It made for a really great way to keep track of where you are in the process as you go. and being able to bounce around to each heading in the “outline” made it easy to combine things into notes that were further up the page.
Essentially you’re baking brownies, or cooking a sheet of meth (as one does), and then cutting it up into serving sizes.