Quick Books Pro Question: I Need Tips On How To Transfer General Deposits Into Customer Payments.?

Hello, We have always entered our invoices in Alpha 4, but for tax purposes we entered our payments in QuickBooks so we’d have a report of our income. The payments were entered as general deposits not as costomer payments because there were no costumer invoices to apply them to in QB.
Then in Oct. 2006, we decided to start using QuickBooks for our costumer invoices & began entering client payments as client payments instead of general deposits. #1 Can we switch general deposits into customer payments or do we have to go in by hand and delete each general deposit and then re-enter it as a costomer payment? #2 If we do switch them over won’t all the reconciliations be off?
Any helpful advice and insights would be gratefully appreciated. Thanks!!!