Hi Jerry, Thanks for sending an MWE, but I think the implication is they should be compilable code. Yours is merely a paraphrase. So I cant see the error you are referring to.
There's nothing special needed, as using Frescobaldi has nothing to do with it. Put your multiple scores inside a \book part. Simple. No special recoding required. You may have some other fundamental problem, hard for me to see. Andrew