Fields created in PHP have never appeared in the admin to edit. I’m unsure how you were getting them to do so. If the groups do exist in the database then creating them also in PHP has no effect, if the field group key already exists or the field key already exists then trying to add them with PHP is ignored. Also, when importing a field group, if the field group key already exists then the JSON import will also be ignored. If you want to be able to continue editing the fields then they must be created in the ACF admin only. Like I said, I have no idea how you would have been able to do what you say you were doing.
