The best way to factory reset a DEP device is to do the following in the Control Tower:

1. Settings > System > enable Re-enroll Apple devices in the previous device group > Save
2. Devices > click on the name of the device group > put a check in the box next to the iPads you wish to factory reset > Select the Erase Device button at the top of the list.
1. Enable Clear Activation Lock
2. Enable Delete Devices from Control Tower 

Once the device factory resets, follow the prompts and the device will be enrolled back into the Control Tower.