There isn’t any way to do this. Once a field group is edited and saved on a child theme it will override the parent theme, as you have seen.
There isn’t any way that I know of to accomplish what you want to do, because there is no way to know what has or has not been changed in the child theme.
The only way to have a parent theme that you can update as well has child themes that can be modified you would have to have field groups in the parent that cannot be modified by setting the “private” flag in the JSON files for these groups and then add new field groups in the child theme for modifications.
