To reconcile commission for a booking duplicated in both travel systems without payout in Tern, you should:
Log the supplier payment in Tern.
Set "Eligible for payout" date to future for tracking without immediate payout.
Set "Payout status" as unpaid to prevent immediate payment.
Modify "Amount received" field if necessary.
You may want to mark the booking as received for record-keeping or set commission to zero for no payout liability.