Reconcile the Original Batch Payment

The full amount that was withdrawn from the bank account should be reconciled against the original payment in Inn-Flow.

This maintains alignment between the bank statement and the transaction record.

Record the Refund as a Separate Transaction

Since the vendor refunded part of that amount later, the refund should be treated as a new incoming transaction, not a void of the original payment.

You should create a separate deposit/refund transaction to record this. This can be done via the Register page > Add Transaction. 

Why not void?

The bank withdrawal was real, and the money did leave the account as a lump sum.

Voiding a payment usually implies the money was never sent—which is not true in this case.

Recording the refund separately ensures the audit trail remains accurate and that the bank reconciliation reflects actual movement of funds.