Try this:

1. Open the affected deposit.
2. Make a fake/temporary manual entry using a Miscellaneous Income account (no "From" entry) in the amount of this payment.
3. Delete the incorrect payment.
4. Click SAVE on top left - DON'T Save and Close.
5. Go to the payment window, make changes, save and exit.
6. Go back to the deposit, delete the temporary entry, click PAYMENTS at the top.  You should see the edited payment.  Click to add that.  Save the deposit.