@NumbersNC 

"If you test it out by making the journal entries that the app made (earlier post) - and make a bunch of them - I think you will find you have to select each line, apply a credit, then select the next line, apply a credit, etc."

You don't need to apply the credits line by line.  Check all the invoices (A/R debits) first, then click 'Discounts and Credits' or 'Apply Credits' once, and then check all the credits.  OK, so maybe not one fell swoop, but this shouldn't take long even with hundreds of transactions.