TuneFab Apple Music Converter can keep the audiobook chapters in the converted M4A file. Simply put, you need to select M4A as output format if you want to preserve the chapter info of your audiobooks.
Go to "Options" and select "Metadata tags".
And then select the "M4A" as output audio format.
After the audiobook is converted as M4A file, you can open the M4A audiobooks via iTunes. When playing the audiobook in iTunes, you will see a drop-down menu called "Chapter" at top where you can browse and select the chapter from.