My Word manuscript numbers its chapters automatically, and the import lost the chapter numbers or got the order wrong. Is that fixed?

Yes, from version 1.9.24. Chapters that Word numbers by itself (the numbers are added by Word's numbering and are not typed in the text) are now found when you import the manuscript (Library, Import), and they are kept in their order. Import the manuscript again with version 1.9.24. In an older version, type the chapter headings into the text in Word (for example "Chapter 1"), save, and import that file.