Procedure for discontinuing the demat for private limited compan

My earlier colleague had applied to NSDL for demat of shares of a Private Limited company.  But later on the company was unable to pay the bills of R&T due to lack of funds.  And so the further procedure of handing over the sharecertificates were not done. The NSDL is raising the bills on the company which the company has paid for one year.  Please advise how to discontinue this and avoid the bills being raised on the company.