create an expense account called clearing
Make a deposit for the amount of the returned ach, use the clearing expense account as the source (from) account for the deposit
Enter a new ach transaction, use the clearing expense account as the expense for the transaction
when you recon, check off this deposit against the original ach payment
the clearing account will be zero, the bill is still paid, the 1099 total has not been impacted, and the recon is fine