SK is a well known abbreviation for Shaikh, thus I would say there will not be any problem in your counselling sessions. But if you want to be safe then you can keep a Gazetted Officer attested copy statement which will certify that the name with Sk and Shaik both the names belong to the same person. For this you can reach out to your DM or Depty. Magistrate and they will do it for you. But in general there are no big problems about it but its better to be safe.

To know more about NEET counselling visit the link below:

https://medicine.careers360.com/articles/neet-seat-allotment

I hope this answer helps. All the very best for your future endeavors!