What's the best solution to ensure E-commerce accounts integrity

Hi, I'd be very grateful for any input to my question.    Sorry, in advance, as it is likely to be a very badly framed question.  I have a client who runs an e-commerce business that has 'agents' and pays commission.  They have an automated system that captures all the data of income, commissions etc.  The data could, in theory, be changed by the administrators so auditors have indicated they would not be willing to sign off on accounts that relied on the commission balances from the e-commerce system.  They are essentially requesting that the data be duplicated in an accounts system with creditors accounts being opened for each agent.  I've looked at a few systems that claim to integrate e-commerce sites and accounts packages but they seem to focus on product based e-commerce with the emphasis on the availability of inventory data and none mention how they work in terms of sales, purchase ledgers.   They also don't mention how they cope with a situation of lots and lots (possibly millions) of online clients and how an accounts package might cope with running out of ledger capacity.