Thank you both for your responses to my questions. Question #2 has been resolved. I was applying a font, Chaucer which has no italic style, but the program was reading it as italic rather than regular.
Question #1 is still alive. The two chapters in question are both .indd files which are fully integrated in the book panel. However, each of them also appear in my documents file as Lock Files. I do not know what that means, as I do not know what a .idml file is, or how to export a file in that format. I can copy those file extensions, but am unable to paste in this window. Perhaps I should just try to delete those Lock Files?