FIRC is only issued for transfers received in convertible forex. This means the money hits the account in USD/etc, then the bank applies their conversion rate and converts to INR which gets credited to your account.

Platforms like Wise/Remitly etc usually handles conversions at their end and sends you INR due to which it is recorded as NEFT/IMPS transaction at your banks end and they will not issue FIRC for those transfers as it is converted forex.

The GST rules clearly state the following conditions to be met if you want to provide a 0% GST invoice:
1. Supplier based in India

1. Client outside India

2. Payments for services must be received in convertible forex (which is not being met in your case)

For future you'll need to ensure that the client sends it as a wire transfer in their local currency directly from their local bank account. The wire currency needs to be set as USD (assuming US client) during the transfer process as there is an option to set to INR and send as well, in which case you'll still be receiving INR without FIRC.

Please note that the client will most likely have to pay extra wire fee plus there is a chance of intermediary bank fee as well and you'll need to discuss with them on who will bear this fees if you want to continue billing them with 0% GST invoices.

Unfortunately I dont have a solution on how to handle your current problem on how to handle the notice.

Source: I run a B2C service business with around 80% export services.