Considering the representation, CBEC has clarified various refund related issued vide Circular No. 147/03//2021-GST dated 12th March, 2020 where following issues are clarified:

Clarification in respect of refund claim by recipient of Deemed Export Supply,
Extension of relaxation for filing refund claim in cases where zero-rated supplies has been wrongly declared in Table 3.1(a),
The manner of calculation of Adjusted Total Turnover under sub-rule (4) of Rule 89 of CGST Rules, 2017.
1. Clarification in respect of refund claim by recipient of Deemed Export Supply
Issue:

As per third proviso to Rule 89(1) of CGST Rules 2017, in case of deemed export, refund application can be filed by either of the following person:
the recipient of the deemed export supplies, or
the supplier of deemed export supplies in cases where the recipient has not avail input tax credit on such supplies. For this purpose, the supplier is required to furnish an undertaking to the effect that the supplier may claim the refund.
With respect to refund by recipient against deemed export, CBEC issued a clarification vide Para No. 41 of Circular no. 125/44/2019 – GST dated 18/11/2019. In such a circular, CBEC placed a condition that the recipient of the deemed exports shall be entitled to refund only with respect of invoices for which he has not claimed any ITC. Therefore, according to this circular the recipient of deemed export supplies cannot avail ITC with respect to invoice for which refund application is being filed.
Following the same, the recipient did not avail any ITC for such inward supplies while filing GST returns.
However, supplier filed representations that the system is not allowing them to file a refund application unless the claimed amount is debited in the electronic credit ledger. Therefore, while filing refund application system was debiting the refund amount in electronic credit ledger
Therefore, credit ledger was debited, however, such amount was never credited in credit ledger causing loss to the person.
Clarification:

Wide circular No. 147/03//2021-GST dated 12th March, 2020, CBIC clarified that 3rd proviso to Rule 89(1) of CGST Rules, 2019 don’t place any condition that the recipient of deemed export can’t claim ITC for invoices for which he will be claiming refund.
Further, to avoid any dual benefits to the claimant, GST portal allows refund of ITC only after debiting the claimed amount from electronic credit Ledger. Therefore. Whenever a refund application is filed for any ITC amount, the system debits the claimed amount to electronic credit ledger.
To avoid hardship to the recipient of deemed export, CBIC removed the condition of non-availment of ITC by the recipient of deemed export. Following clarification is inserted vide amended pare:
3rd proviso to rule 89(1) of CGST Rules allows refund of taxes paid on deemed export to either the recipient or the supplier.
Where refund is sought by the supplier, the documentary evidence as specified in notification No. 49/2017- Central Tax dated 18.10.2017 are required to be furnished. Further, an undertaking is also required that the recipient of deemed export supplies shall not claim the refund in respect of such supplies and also shall not avail any input tax credit on such supplies.
Similarly, where refund is claimed by the recipient, he is required to submit an undertaking that refund has been claimed only for those invoices which are mentioned in statement 5B* and the amount does not exceed the amount of input tax credit availed in the valid return filed for the said tax period.
The recipient shall also declare that the supplier has not claimed refund with respect to the said supplies.
* contains details of deemed export invoices for which refund is being claimed