Shaykh al-Islām Ibn Taymiyyah [d. 721 AH] said:

What was mentioned by Allāh, the Most High, in the verse that guides towards arguing with the People of the Scripture in a way that is best, except for those who commit injustice among them, is a fully actionable passage, free from abrogation. This is also the case with what the Most High has alluded to from arguing with any individual from the creation as a whole:

ادْعُ إِلَىٰ سَبِيلِ رَبِّكَ بِالْحِكْمَةِ وَالْمَوْعِظَةِ الْحَسَنَةِ ۖ وَجَادِلْهُم بِالَّتِي هِيَ أَحْسَنُ ۚ إِنَّ رَبَّكَ هُوَ أَعْلَمُ بِمَن ضَلَّ عَن سَبِيلِهِ ۖ وَهُوَ أَعْلَمُ بِالْمُهْتَدِينَ ‎﴿١٢٥﴾‏

‘Invite to the way of your Lord with wisdom and good instruction, and argue with them in a way that is best. Indeed, your Lord is most knowing of who has strayed from His way, and He is most knowing of who is [rightly] guided.’
[Al-Naḥl, 16:125]

For, indeed, among the creation are those who claim that the verses that encourage debate and evidence-based discussion with the disbelievers has been abrogated with the verses that command war. Their thinking is that a legislative order of physical contention cannot coexist with a legislative order of debate. This is a clear mistake. For abrogation of a ruling occurs only if the abrogating rule completely contradicts the abrogated law, like the contradiction of the order to face Masjid al-Ḥarām [in Makkah] for ṣalāh with the order to face Masjid al-Aqṣāʾ in Al-Shām, or the contradiction between the obligation of fasting for the resident [not travelling] with the order of him possessing a choice between fasting and feeding the poor for every day of obligatory fasting, or the contradiction in the impermissibility of exceeding the set limits for the portions allotted to inheritors with the order to bequeath a portion of inheritance to parents and close relatives, and the contradiction in the [initial] order to stay one’s hand from war with His saying: ’fight them’ as the Most High says:

أَلَمْ تَرَ إِلَى الَّذِينَ قِيلَ لَهُمْ كُفُّوا أَيْدِيَكُمْ وَأَقِيمُوا الصَّلَاةَ وَآتُوا الزَّكَاةَ فَلَمَّا كُتِبَ عَلَيْهِمُ الْقِتَالُ إِذَا فَرِيقٌ مِّنْهُمْ يَخْشَوْنَ النَّاسَ كَخَشْيَةِ اللَّهِ أَوْ أَشَدَّ خَشْيَةً ۚ ‎﴿٧٧﴾‏

‘Have you not seen those who were told, “Restrain your hands [from fighting] and establish prayer and give zakah”? But then when fighting was ordained for them, at once a party of them feared men as they fear Allāh or with [even] greater fear…’
[Al-Nisāʾ, 4:77]

So His order to fight them abrogates the previous directive of restraint. As for the saying of the Most High:

ادْعُ إِلَىٰ سَبِيلِ رَبِّكَ بِالْحِكْمَةِ وَالْمَوْعِظَةِ الْحَسَنَةِ ۖ وَجَادِلْهُم بِالَّتِي هِيَ أَحْسَنُ ۚ ﴿١٢٥﴾‏

‘Invite to the way of your Lord with wisdom and good instruction, and argue with them in a way that is best’
[Al-Naḥl, 16:125]

And His saying:

۞ وَلَا تُجَادِلُوا أَهْلَ الْكِتَابِ إِلَّا بِالَّتِي هِيَ أَحْسَنُ إِلَّا الَّذِينَ ظَلَمُوا مِنْهُمْ ۖ ‎﴿٤٦﴾‏

‘And do not argue with the People of the Scripture except in a way that is best, except for those who commit injustice among them’
[Al-ʿAnkabūt, 29:46]

These directives in no way contradict the order to fight and strive against those among them who have been ordered as such. However, the command to fight, [once issued], contradicts only the order of restraint and being satisfied with only debate.

Source: Al-Jawāb Al-Ṣaḥīḥ: 217-219
Translated by: Riyāḍ al-Kanadī