Scope

Which currency will the chargeback happen in if I have two currencies configured for my website?

Is there any specific setting for it?

Note: Chargeback automation feature is currently available only on selective plan. Please check the plan and pricing page. 

When chargeback automation is enabled, you can configure the setting to handle invoices, subscriptions, other subscriptions related to the customer as well as transactions.  The payment gateways handle the refund. Based on the input from gateways, Chargebee handles invoices, subscriptions, and transactions related to the customer. 

The amount communicated to Chargebee on this flow by the gateway will be of the initial transaction currency (as per the invoice)

So even if you are using more than one currency, the respective invoice's currency will be used for the refund as well.

To know how Stripe handles dispute amount refer to this link