The way to look at this is to consider the PayFast account as a second business bank account and payouts are just a transfer of funds from one account (the PayFast one) to another account (your bank one). This means that all you need to recon is to ensure that the payouts requested from the PayFast account match the payments received to the bank account.
To recon each individual transaction, match your shopping system to each order that was processed.
Together, these two steps ensure that all funds are accounted for and reconciled.
The running balance on the PayFast account provides additional confirmation that all funds are accounted for.
We do not directly match individual transactions on our side to each payout so it is not likely to match very often. There are more considerations than just the timing and retained balance amounts and we allow payouts for any chosen amount so there is no direct link from transaction to payout.
Update: On request, merchants can implement a Settlement Recon feature to simplify the recon process. This feature adds two new columns to the payments dashboard: Batch ID and Retained. The Batch ID displays the transactions history and Retained displays the current balance. This enables merchants to know exactly which payments are included in the payout.
The information displayed in these two columns allows you to ensure that the payouts you requested from your PayFast account match the payments received in your bank account. Therefore, your payout and your retained balance should equal all transactions received with that Batch ID.
The Settlement Recon feature only works on the condition of the full available balance being paid out with each payout.
If you would like to enable the Settlement Recon feature, contact merchantsupport@payfast.co.za.