Somehow, the GoCardless fees need to be included in the transactions to avoid leaving an accounting black hole as GoCardless doesn't invoice merchants like card processing companies do, they just take their fees right out of your transaction, and that's it.
So, somehow, WHMCS needs to include this in the sales reports to show the costs of the transactions.
In speaking with Gocardless support, there is another endpoint you could use that might suit your purposes.
You can get this information from the payouts_items endpoint
https://developer.gocardless.com/api-reference/#core-endpoints-payout-itemsIf the deducted fees endpoint that I mentioned before doesn't work for you, this one might be workable into your flow.
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Thanks for taking the time to submit this idea. At present WHMCS uses the GoCardless Payments API (https://developer.gocardless.com/api-reference/#core-endpoints-payments) which unfortunately doesn't return transaction fee information. This is why that information isn't available in WHMCS today.
The alternative API endpoint being suggested here, does look to have this fee available, when it's paid-out to your creditor account later on. This is potentially something we can consider if other users support this.