Praise be to Allah.
Shaykh `Abd Al-`Aziz ibn Baz (may Allah have mercy on him) said:
There is nothing wrong with that. The Du`a of Qunut is Sunnah and the Prophet (blessings and peace of Allah be upon him) used to recite Qunut . He taught Qunut and the words of Qunut in Witr to Al-Hasan (may Allah be pleased with him), so it is Sunnah.
If you recite Qunut in Witr every night, there is nothing wrong with that, and if you omit it on some occasions so that the people will know that it is not obligatory, there is nothing wrong with that either.
If the Imam omits Qunut on some occasions so that the people will know that it is not obligatory, there is nothing wrong with that. When the Prophet (blessings and peace of Allah be upon him) taught Al-Hasan (may Allah be pleased with him) Qunut, he did not tell him to omit it on some days . This indicates that if he does it persistently, there is nothing wrong with that.
And Allah knows best.
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