Hello - I have the same issue described on this thread.  I've followed all of the instructions (created the bad check charge item and income account, recorded journal entry to accounts receivable, unapplied the merchant payment from the original invoice and applied instead to the journal entry, even deleted and re-recorded the deposit), with the same issue described here.  The new invoice shows the correct balance due amount (in my case $1160, original $1150 plus the $10 returned ACH charge), but the ACH payment link on the invoice will not allow a payment amount greater than $10. 

I confirmed the detail in my merchant account transaction is the same as the screenshots.  In my case, it appears the customer used an incorrect routing number, so their bank didn't honor the ACH/echeck payment. 

I also followed the update instructions (my file was current, but ran anyway) and the verify data (no errors exist), and the issue remains - in theory this process should work, but something in the background "remembers" the original payment and won't unapply it. 

I think we need another workaround.