6.
It is not in dispute that all the invoices are to be uploaded by the supplier in GSTR-1 on the basis of which ITC is reflected in GSTR-2A. You are to pursue your supplier to upload the invoices. The Common Portal System will allow ITC whichever is reflected in GSTR-2A.If the supplier does not upload the invoices in GSTR-1, the buyer is not at fault at all. The basic conditions of availment of ITC are :
1.Tax invoice
2.Tax paid character
3.Utilization of input/input services in the course of business and furtherance of business.
If you fulfill above conditions, your substantive right cannot be snatched. The buyer cannot suffer on account of lapse committed by the supplier. Recently there were decisions of various Courts in favour of the assessees on this very issue. The compliance with GST laws is to be preferred to Common Portal System. Relief is possible in two ways:-
1. Through litigation.
2. The Govt. should frame a law to enforce the supplier to upload invoices within a stipulated.
This problem is already in the notice of the GST Council. The new format of returns may solve this problem being faced by so many tax payers.
At present best option for you is to persuade your supplier to upload invoices so as to enable you to file Annual Return correctly. The last date of Annual Return is likely to be extended for the purpose of updation of GSTR-2A.