TCS which is deposited by the E-commerce operator into government account will be reflected in the cash ledger of the registered supplier (on whose account such collection has been made) on the basis of the valid return filed by the E-commerce operator. The same can be used at the time of discharge of tax liability in respect of the supplies by the registered supplier.
(ICAI FAQ PUBLICATIONS 06-09-2017 TAX PAYMENTS, INTEREST, PENALTIES AND OTHER AMOUNTS: FAQ NO. 60)