Dear Shivkumar,
Your query has two issues
1) You have not charged service tax to your client who is operating in SEZ
2) You have input service tax credit against services provided to your above mentioned client.
To clerify you
1) You need to obtained "Form 2" from your client and on the basis of that you are not require to charged service tax to him for the services you billed. Form 2 is issued by service tax department to the unit operating in SEZ. Form 2 will have a mentioning of your company Name and services against which you need not charge service tax.
2) You can take the Input service tax credit paid on Input services. Rule 6(3) of CENVAT credit rule prescribed the reversal of Input tax/duty incase of service provider provide taxable as we as Exempted services. However your service to a unit in SEZ shall not be considered as exempted hence the said rule shall not applicable to your case.
Hope above will clear your doubt.
Regards
Dharmesh
8898507555