بسم الله الرحمن الرحيم
(Fatwa: 730/853/L=8/1439)
In such situation the Hanafi should read Dua-e-Qunoot, but he should not supplicate raising his hands.
وَيَتْبَعُ الْمُؤْتَمُّ قَانِتَ الْوِتْرِ أَيْ وَلَوْ كَانَ الْإِمَامُ شَافِعِيًّا يَقْنُتُ بَعْدَ الرُّكُوعِ لِأَنَّ اخْتِلَافَهُمْ فِي الْفَجْرِ مَعَ كَوْنِهِ مَنْسُوخًا دَلِيلٌ عَلَى أَنَّهُ يُتَابِعُهُ فِي قُنُوتِ الْوِتْرِ لِكَوْنِهِ ثَابِتًا بِيَقِينٍ (منحة الخالق / 2/ 79/ ط زكريا ديوبند)
Note:It should be noted that if an imam leads witr salah with two salam other than Haramain then a Hanafi muqtadi should not pray behind him.
Allah knows Best!
Darul Ifta,
Darul Uloom Deoband