I just tried duplicating the field group you supplied. I didn’t look at every field, but all the nested repeaters seemed to duplicate properly.
When you say
I also noticed that ACF plugin is unable to update the JSON file for the field group and instead it is creating a new one with the new flexible content on it.
This would be normal. Duplicating a field group is creating a new field group. Once it is duplicated it is separate from the original. Are you expecting that updates to one version of the field group will be copied to the second version?
