As you said, this boils down do the field keys being identical. This is how ACF keeps them in order. Now that you’ve got duplicates you’re going to have a hard time doing anything with either of these groups. The only way you’re going to solve this is to delete the second group and hope that it does not hurt anything.
ACF5 has the ability to duplicate field groups and not have this problem. If you do something similar at some time you can just change the field keys first, for example, something as simple as adding ‘x’ to the end of each one will prevent this.
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