In your case you will need json folders for all of the sites.
In the parent theme you will have the field groups where everything is identical on all sites. You can create a function/action in the parent theme to add this “load point”. You can only work on and edit these field groups in the admin of the site that is using the parent theme.
Then you will have 2 child themes, one for each site. These will have their own json folders. You only edit the field groups in the admins of these sites where the field groups are not identical.
Your other choice is to keep all of the field groups, the ones that are the same and the ones that are different in the parent theme and instead of creating a load point for ACF you would build your own function to add the field groups to a site. In this function you would look at the site currently being loaded and only include the field groups you want to apply to that site.
Hope some of that makes sense.
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