It is permitted to recite a part of the Surah, especially with long surahs, in one Rak’ah of Salah and in the next Rak’ah, skip to a different part of the same Surah. Ibn Abideen رحمه الله تعالى mentioned this in his Haashiyah. However, he said it is better not skip from one part of a Surah to another without a need. He considered it ‘Khilaf al-Awlaa’, which means it is better not to.
It is not Makruh, as long as one does not miss out a single Ayah. For example, if a person recites verses 90-99 in the first Rak’ah, and in the second recites from verse 101 onwards, that would be a problem. This is because he has missed out one single Ayah (verse 100), therefore that would be Makruh.
قَوْلُهُ وَلَوْ مِنْ سُورَةٍ إلَخْ) وَاصِلٌ بِمَا قَبْلَهُ أَيْ لَوْ قَرَأَ مِنْ مَحَلَّيْنِ، بِأَنْ انْتَقَلَ مِنْ آيَةٍ إلَى أُخْرَى مِنْ سُورَةٍ وَاحِدَةٍ لَا يُكْرَهُ إذَا كَانَ بَيْنَهُمَا آيَتَانِ فَأَكْثَرُ، لَكِنْ الْأَوْلَى أَنْ لَا يَفْعَلَ بِلَا ضَرُورَةٍ)
(رد المحتار على الدر المختار في شرح تنوير الأبصار المعروف بـ (حاشية ابن عابدين
(His words and even if it is within a Surah) Continuing with what is before it, meaning if he recites from two places and moves from one ayah to another part within one Surah it is not disliked, if between them is two Ayah or more. But it is more preferred that he does not do it without necessity. – (Haashiyah Ibn Abideen)
Answered by Shaykh Noor ud-deen (04.01.2021)
Can you recite Surah Ikhlas instead of Dua Qunoot in Witr Salah?