Thank you so much for your very helpful response! These data fill in some of the gaps I had, and I have now obtained his will.
It looks from some of the first names in your search results, that he may have had some descendants that stayed in Java. His will, however, mentions only the three children in my first posting, who were put under the guardianship of their uncle Arthur Thomson, a ship and assurance broker in Aberdeen. Harvey's only son was fathering children in Aberdeenshire in the 1850s (including a Harvey and an Antoinette). Perhaps the name Antoinette was more common in Java than Scotland at the time and it's a coincidence.