Are you using the update_field()
function to set the value when you populate the custom fields during import?
If so, are you using the field_key
value such as:
$field_key = "field_5039a99716d1d";
$value = "some new string";
update_field( $field_key, $value );
Full docs: http://www.advancedcustomfields.com/resources/update_field/#finding-the%20field%20key