Just guessing it sounds like you have used configurator on this iPad before it stopped showing in Prepare. So most likely you have supervised this iPad, and now it will only show up in the Supervise tab.
Have only the iPad in question plugged into the Mac, go to the Supervise tab and click USB connected devices on the left hand side. If an iPad is in that list, there it is. If you would still like to wipe it and start fresh, right click (or click with two fingers at the same time, depending on your settings) on the iPad and a drop down menu will appear. Click on 'Unsupervise'. That will wipe your iPad and unsupervise it, as if it was a brand new iPad that had never been plugged into Apple Configurator.