In case I didn't already have enough reasons not to be in the payment processing business.  Here's another one.

My (limited) understanding is that any payments that get sent with the efile get shuffled off to a different department.  The only way to cancel them is to call that department.  So my guess would be (like Lisa said) that if you submit another 1Q-ES payment with the amended return it will ADD to the EFT queue (and then be taken along with the originally scheduled EFT).