Answered by Shaykh Hamza Karamali, SunniPath Academy Teacher
I am in the process of making up missed prayers and they are many in number. In order to speed things, I pray one rakat of witr after Isha. Is praying one rakat of witr acceptable in the Shafi’i madhab?

In the Name of Allah, Most Merciful and Compassionate
Witr vs. Makeups
In the Shafi’i school, one does not pray any non-obligatory prayers if one has obligatory prayers to make up. Praying witr was the Prophet’s (Allah bless him and give him peace) inveterate practice and its performance is strongly emphasized, but it remains a sunna prayer. As such, it should be omitted and replaced with a makeup prayer instead. For more details on the fiqh of making up missed prayers, see:
Making up Missed Prayers
http://www.sunnipath.com/resources/Questions/qa00001801.aspx
Note that other schools differ on this issue, holding it superior to pray the witr prayer even when one has many makeups to make up.
One-Rak’ah Witr
It is valid to confine oneself to praying one rak’ah of witr. However, to make this a habit is disliked (Bushra al-Karim, 1.113, Mustafa Babi al-Halabi).
And Allah knows best.
Hamza.