I searched for this extensively before adding this. Note, this applies only to macOS. I do not have a Windows system to verify.
I, too, struggled to get chapter numbers for the middle chapters of my book during a compile (in this case, to Word or PDF). The solution I stumbled on requires nothing special. I have my book structured as follows:
Book
Part
Chapter Heading
Chapter Text
…
Once on the Compile screen, select the entire manuscript and check everything (Option-click). Then, select the Part needed. The compile will start with the correct chapter numbers, assuming you have “Chapter <$t:chapter>” (or the like) in the chapter heading.
If any parts or chapters are not selected when selecting the entire book, once you select a part, the numbers will start with Chapter One. This only took a couple of hours to figure out, and it not i any other post that I can find.
I’m willing to make a video if needed.