"Can we use Internal Voucher for credits? But I think we should enable this only to the online warehouse and not the other stores. Is that possible?"
Yes - the "Internal Voucher" payment type can be setup (similar to screenshot from our test store below) to enable the payment type (in online only) without allowing it to be used in POS.
If/when you have the payment type setup, would you/accounting prefer Shopify store credit refunds be mapped to it?
REX knowledge base link: https://galaxy.maropost.com/kb/articles/590-configuring-payment-types
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