Is there sin upon one who is assailed by negative thoughts regarding the answered prayer – despite his certainty and trust in Allah – or is there nothing upon him as long as he dislikes these thoughts?

These whisperings (waswas) will not harm you as long as you detest and are repulsed by them. Indeed, your aversion to them is a sign of the sincerity of your faith. So strive against them and do not give in to them. Know that Allah's choice for you is better than your own choice for yourself. He may withhold from you what you love for a great benefit, and "Allah knows while you do not know." You will never be deprived of good through supplication (du'a), for either your request will be granted, or Allah will protect you from evil, or He will store it for you on the Day of Resurrection. So trust in Allah's planning and choice, entrust your affairs to Him, and be content with His decree, for therein lies happiness.