You can connect multiple Shopify stores to 1 Xendit account.
However, please be noted that you won’t be able to differentiate the order between the stores since the reference ID would be reconciled in the same format on Xendit Dashboard and it’s uneditable from Shopify.
You can refer to this article, for more information on how to reconcile Shopify orders on Xendit Dashboard.
For more information on how to integrate your Xendit account to Shopify, please refer to this article. If you happen to have integrated your Xendit account to the first store and are unable to do it via your Xendit Dashboard for the second store, you can install Shopify through this link. Make sure you’re logged in to the right Xendit account and Shopify store when doing so.