Commissions are tracked almost instantly after Shopify marks an order as paid. If that order is later refunded or cancelled, the commission is not removed automatically — that's a manual step today.
To remove it, open the ambassador's detail page, find the sale, and delete that commission. It updates their balance right away, so it's worth doing before you pay them out. Here are the exact steps: How to delete or remove an ambassador's commission.
If refunds are a regular part of your business, it's a good idea to cover them in your ambassador terms — and to keep an eye on ambassadors with an unusually high refund rate.