If you have multiple different bank accounts in different currencies, the balance for each currency is handled separately. Stripe will not subtract from payments received in one currency to cover a negative balance in another currency.
In order to bring a balance in a non-default currency out of the negative, you will need to create a manual payout using the Stripe API or from your Dashboard, with the currency specified as the non-default balance currency. The funds will undergo currency conversion and will deposit into your default bank account in your default currency.
If you have questions about this process or are unable to complete this conversion using the API or Dashboard, contact Stripe Support.