I think you may be running into issues because you are working on parent/child themes on the same site, same db tables.
When I do this I do it on a multisite setup. One site is set up to use the parent theme and this is the only place I edit field groups in ACF. A second site is set up to use the child theme and I do not edit field groups on this site. If I do, then they only apply to the child theme and do not effect the parent theme. You could also do this on multiple sites.
