Chris,
I just made a payment in my Sandbox for 6 invoices/credit memos.

You can see I highlighted the Payment Line for the payment and clicked Process/Unapply Entries. It opens the Unapply Customer Entries page. I will now highlight all the rows to Unapply them against the invoices/credit memos leaving the payment open.
then all my Invoices/Credit Memos and the Payment show a remaining amount. 
Now you can reverse the payment, since it was a duplicate.
Hope this helps.
Thanks,
Steve