These one-off situations have a lot of solutions, and you can choose whatever you want if you feel comfortable with it. 

If I received a payment that was later rejected, I would just delete the payment, and that would restore the balance due for the invoice. For the bank download when that amount comes in and out, I would just click on exclude, if the in/out amounts are the same. 

You could get really detailed in how you treat this type of issue with a huge paper trail, but I don't think it is necessary.