Ibn Al-Jawzi reports that Ibn Abbaas, Al-Hasan, Ikrima, Muqaatil and Ad-Dhahhaak have said that
was abrogated by
Here is what Ibn Al-Jawzi writes about this case,
باب ذكر الآيات اللواتي ادعي عليهن النسخ في سورة بني إسرائيل. ذكر الآية الأولى: قوله تعالى "وقل رب ارحمهما". قد ذهب بعض المفسرين إلى أن هذا الدعاء المطلق نسخ منه الدعاء للوالدين المشركين، وروى نحو هذا عن ابن عباس رضي الله عنهما والحسن وعكرمة ومقاتل. أخبرنا المبارك بن علي قال أبنا أحمد بن الحسين بن قريش قال أبنا أبو إسحاق البرمكي قال أبنا محمد بن إسماعيل بن العباس قال أبنا أبو بكر بن أبي داود قال بنا محمد بن قهزاد قال حدثني علي بن الحسين بن واقد قال حدثني أبي عن يزيد النحوي عن عكرمة عن ابن عباس رضي الله عنهما في قوله "إما يبلغن عندك الكبر" إلى قوله "كما ربياني صغيرا" نسختها "ما كان للنبي والذين آمنوا أن يستغفروا للمشركين". قال أبو بكر وبنا محمد بن سعد قال حدثني أبي عن الحسين بن الحسن بن عطية عن عطية عن ابن عباس رضي الله عنهما "إما يبلغن عندك الكبر" إلى قوله "صغيرا" فنسخها "ما كان للنبي والذين آمنوا أن يستغفروا للمشركين". قال أبو بكر وبنا أحمد بن يحيى بن مالك قال بنا عبد الوهاب عن سعيد عن قتادة نحوه. أخبرنا ابن ناصر قال أبنا ابن أيوب قال أبنا ابن شاذان قال أبنا أبو بكر النجاد قال أبنا أبو داود السجستاني قال أبنا أحمد بن محمد قال بنا عبد الله بن عثمان عن عيسى بن عبيد الله عن عبيد الله مولى عمر عن الضحاك "وقل رب ارحمهما" نسخ منها بالآية التي في براءة "ما كان للنبي والذين آمنوا أن يستغفروا للمشركين".
قلت وهذ ليس بنسخ عند الفقهاء إنما هو عام دخله التخصيص، وإلى نحوما قلته ذهب ابن جرير الطبري
Ibn Al-Jawzi's opinion is that, as the scholars of Fiqh (jurisprudence) have said that this is not abrogation, but specification. He said Ibn Jareer At-Tabarai said something similar.
IMHO, the matter is a lot simpler. God clearly gives in 9:113 the condition for prohibiting Muslims from praying for their polytheist parents when He says "after it has become clear to them that they are the companions of Hellfire." He further explains this in the very next verse,
to give an example from the story of Abraham, peace be upon him. In
God tells us that Abraham promised his father that he will ask God to forgive him. God tells us in
9:114 that Abraham did that but "when it became clear to him that he was an enemy to God, Abraham cut ties with him."
Thus, the two verses together make this consistent instruction,
"
Ask God to be merciful with your parents as they have been merciful to you when you were young, but if it becomes clear to you that they insist on disbelief, then do not ask God to forgive them because God has determined to send disbelievers to the Fire."
If disbelieving parents are still alive, a Muslim child is encouraged by 17:24 to ask God to have mercy on them. The best mercy is to guide them to Islam. But if those parents have died as disbelievers, it is too late to forgive them, and that is what 9:113-114 talk about.
So, with all due respect for Ibn `Abbaas, may God have been pleased with him, 9:113-114 do not abrogate 17:24. 9:113 specifies an exception to the general command of 17:24 and 9:114 gave an example of that. In other words, 17:24 still applies. If 17:24 has been abrogated then what that means is that Muslims no longer have to "lower to their parents the wing of humility out of mercy and say 'Lord, have mercy on them like they raised me when I was young.'" Obviously, that's not the case.
9:113 only says that it is improper for Muslims to ask God to forgive their polytheist relatives. It does not say it's a sin to ask or that they would be punished if they did. The reason it's improper is that God has already decided that the pagans of Mecca are "the companions of the blazing fire."
Dr. Mustafa Zayd's refutation, on pages 112-113 (item 842) of volume 2 of his book النسخ في القرآن الكريم, is that 9:113 is a specification of the generality in 17:24. He probably meant an exception.