Since October 2024 the GST portal has an Invoice Management System (IMS). Each supplier invoice appears there and you can accept it, reject it, or keep it pending. Accepted invoices count towards GSTR-2B, rejected ones are left out, and pending ones wait for a later month. Invoices you take no action on are treated as accepted when GSTR-2B is generated. If you act after the 14th, you recompute GSTR-2B on the portal before filing GSTR-3B. The GST portal publishes the current advisories.
In practice, reconciliation now happens before the IMS actions: match your books first, then accept, reject or park on the portal based on what you found.