Rahul, who didn't feature in the ODI series against Australia, was dropped for the ODIs against New Zealand, while Karn replaced the injured 18-year old legspinner Rahul Chahar after an impressive run for India A against New Zealand A across formats.
Karn picked up 16 wickets in the two unofficial Tests, which India A swept, and collected nine more, including a five-for, in the four one-dayers. In the final match, his unbeaten 38 helped steer India A home in a tense chase.
Karn, who was a late call-up to the India A squad, also picked up two five-fors in two Duleep Trophy matches at the start of the season last month.
Updated Board President's XI squad: Prithvi Shaw, KL Rahul, Shivam Chaudhary, Shreyas Iyer (capt), Karun Nair, Gurkeerat Singh, Milind Kumar, Rishabh Pant (wk), Shahbaz Nadeem, Karn Sharma, Dhawal Kulkarni, Jaydev Unadkat, Avesh Khan.