Masbooq missing dua-e-qunoot with the imaam in witr salaah

He will not recite the Dua-e-qunoot when making up for the missed rakaats. Since he joined the Imaam in the ruku of the third rakaat, it will be considered as though he had recited the qunoot since he got the third rakaat, even though he did not recite the qunoot. Hence, after the Imaam makes salaam he will stand up to complete his two missed rakaats.

After the imaam completes the salaah, he will stand up, recite the sana, ta'awwuz, tasmiyah, qiraat of surah faatiha and surah and will thereafter complete the first rakaat and sit in tashahhud. Thereafter, he will stand up and perform the last rakaat with surah faatiha and a surah and complete the salaah as normal.

And Allah Ta'ala (الله تعالى) knows best.