@NumbersNC 

"The 3rd party app is totally irrelevant at this point"

Well, not totally.  It depends on what customer name the app used for these journal entries (JEs).  What customer name is listed under the NAME column on the JEs?  JEs need to have a name assigned to any entry that hits A/R.  Is it the same name on the payment (A/R credit) as the sale (A/R debit)?  If so, go to Customers > Receive Payments.  Choose that customer name and you will be able to apply the credits to all of the invoices in one fell swoop.  If it's not the same customer name on the journal entries, then you will need to clear them one at a time, going customer-by-customer.