This issue was reported by me on gst greveince and a docket number was issued. Now it has been resolved. The final reply from technical team is as under.
Resolution: Dear Taxpayer, This is regarding your query for the missing Bill of Entry in GSTR-2A/2B. A new self-service functionality to "Search BoE & Query ICEGATE" has been made operational on GST Portal. You are requested to use this facility & initiate query for latest BE version from ICEGATE. The detailed advisory for this functionality is given on GST Portal at https://www.gst.gov.in/newsandupdates/read/505. Live Webinars on this topic is being scheduled by GSTN, please refer to https://www.gst.gov.in/newsandupdates/read/506 for details. A detailed step-by-step manual is available at https://tutorial.gst.gov.in/userguide/taxpayersdashboard/index.htm If you face any other issue, Kindly raise a new ticket with screenshots & detailed description. Thanks GSTN supp. Team
For further assistance, please feel free to contact us at GST helpdesk number 1800-103-4786 or visit Grievance Redressal Portal https://selfservice.gstsystem.in/ to log a ticket.
NOTE:
Please login to your gst account and under SERVICES go to USER SERVICES and then select last option SEARCH BOE. NOTE reference date of BOE is date of OOC. You can fill details and can fetch details from icegate to Gst portal. I have already done it.