Hi Ankita,
It is not clear whether the service tax paid on the service is exempt by way of exemption provided to SEZ units under Notification No.40/2012-ST or vide any other notification.
If it is vide Notification No.40/2012-ST, then the refund route is always open to the SEZ unit.
If it is vide any other notification, then the same shall be claimed first as self adjustment, i.e., you can carry forward this amount without any limit from 1 July 2012 vide Rule 6(4B) of STR, 1994 and then when the liability comes, it can be adjusted.
Secondly, if first option is not possible, you may opt for refund from the Department, but it is really a cumbersome job. I personally suggest don't go this one.