Scriv to rtf and back to Scriv

I created the first draft of a novel in Scriv, then compiled it to rtf (Nisus) for my beta reader. What’s the best way to bring the draft back into Scriv?

I tried cut and paste but the text appears in both the chapter and its included scenes. I tried deleting the text from the chapters but Scriv won’t let me. The edits I make in scenes also appear in the chapters. I’m afraid that compiling to epub will be a mess.

What’s the best way to transfer from Scriv to Nisus and back again?

While in reference to the Final Draft format instead of RTF, the answer to this topic was answered recently, here: Bringing revisions back into Scrivener after compile.