Antonin's task was to reprogram her to become more favorable to the regime, loyal to Lord Voldemort. It had been an arduous process and one that Hermione was aware of every second he was engaged in completing his orders. When it was all over, when she was sympathetic to the plight of those around her who were just simply trying to create a better world for witches and wizards to live and be prosperous, she wasn't confused. She certainly never woke up in the middle of the night thinking she was back in the Forest of Dean with Harry and Ron.