It will still go away after a couple of days, don't worry about it being in the cart you would have to complete the purchase process for it to take effect.
The real problem is not being able to set the item total in the cart to zero. Whilst the cart isn't empty (as you essentially can't empty it) you will get reminders.
I went into the cart to carry out some testing for another forum question relating to the cart/store, I couldn't zero the quantity, it won't let you set a figure less than 1. But the reminder did go away after a couple of days.