I searched to see if this is address already and didn’t see anything.
I use the <$n> designation to number my chapters. When I compile a partial part of my book the <$n> sets itself to 1 for the first instance it is encountered in the compiled chapters, not the first instance it is encountered in my overall book. All chapters are under a Manuscript folder.
I’ve worked around this by compiling each chapter header, but this results in unneeded pages at the beginning the chapters I’m printing for editing.
Otherwise Scrivener is a great product and has helped me tremendously with my first book.