I have run into the same problem.  This is a programming issue that needs to be corrected.  Please enable the bounced check option for e-checks!!  Occasionally, but not often I will have a customer with insufficient funds and the check bounces.  I need the same process to occur for e-checks as it does for normal bounced checks.  The amount is deducted from the bank account register, along with any fees which I can enter.  I can also create an invoice to charge the customer the return fee and Quickbooks automatically activates the invoice as unpaid again.  I am well aware how to manually delete the deposit, delete the payment, change the payment to a regular check, then re-add the payment to the deposit, then use the bounced check button and finally have it enter a journal entry, and charge the customer and create an account and item list to deal with all of these things, but the point is we have programming for a reason!  Please FIX this and enable the bounced check button for e-checks.