Rejection of new Application

There is no limit for asking but practically one time and thereafter deptt. Reject application

If the department must be satisfied according to their need we must file the documents

In the case where the proper officer is of the opinion that the amendment sought is either not warranted or the document furnished therewith are incomplete or incorrect, he may ask Registered person to show cause within 7 working days of the service of the notice.

Dear Ujwal :
As per Rule 9 of CGST act , when officer found any deficiencies in application submitted by person , the notice is issued to Applicant in form Reg-03 & Applicant has time period of 7 days to furnish the clarification, doucment in Form Reg-04 .
and if the officer not satisfy with clarification furnished by the Applicant can be reject the application by giving reason in writing .

So if your application is rejected or you have file clarification , it's better you go & meet to proper Officer can clarify the same.