RCM Liabilities Should Pay as per Books or GSTR-2B -- confusion

Sometimes RCM Supplier Not Uploaded their Invoices within Stipulated time

Due to above reasons Actual RCM Liabilities Not Reflected in GSTR-2B

Example : For April -- Actual RCM Liabilities as per Books -- 5000/-

But GSTR 2B Reflected is Rs. 2000/- due to Non uploaded by Supplier

Question : Which RCM liabilities We have to pay ??? 

Actual Liabilities of Rs. 5000/-  or GSTR 2B Reflected Liabilities of Rs. 2000/-

Please reply in details