Is it permissible to combine intentions for the Sunnah prayer of 'Isha', Shafa', and Witr, and if not, is there any harm in praying the Sunnah of 'Isha' and then performing Witr with one Rak'ah?

It is not prescribed to combine the intention of the Sunnah (supererogatory prayer) of 'Isha' and the Shaf' (even-numbered prayer preceding Witr) in two rak'ahs (units of prayer), because each has an independent intention. The worshipper can pray Witr with one rak'ah after the Sunnah of 'Isha'. It is better to pray two or more rak'ahs (4, 6, 8, 10 rak'ahs) before the single rak'ah of Witr; this is what is called Shaf'. The minimum for Witr is one rak'ah, and the maximum is eleven rak'ahs, and the lowest complete number is three rak'ahs.