With the Credit Invoice Feature enabled each credit that is generated has a corresponding invoice generated. A credit invoice with an "Open" status indicates that there is a remaining balance. These balances will be reflected on under the customer's Account Information.
To export your customer's account balances you'll want to use the Invoices - Summary Export with the following configuration:
Once exported, you can sort by "account_code". This will group all open credit invoices together to allow for quick calculation. Once sorted you'll take the total of the "invoice_balance" column for each account code to see the customer's account credit balance.