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I've used the 2 window method and dragged and dropped in the past. It's ok for doing relatively small numbers of notes, but still clumsy. With the hundreds of notes I'm looking to sort and organize, looking for something that will speed this up. Currently looking atporting out to markdown, organizing with file organization tools in Windows, and then maybe porting back in.
I scripted some stuff like mass export ( https://github.com/projectje/OneNoteExporterAkaPublisher ) but did use the com api.