In CUCM Under Device>Phone find the device you wish to remove the LINE from. On the phone configuration page click the Modify Button Items button.
On this page you can select a LINE and click the arrow to move it into the "Dissociate These Items" box. This works for any line that is NOT LINE 1. In later version of CUCM that became a Fixed Feature button so if you want to change LINE 1 you have to go into LINE 1 on the phone configuration page and just update the directory number settings to be what you want them to be. But Line 2 and beyond you should be able to just Dissociate the line.This only remove the LINE from this device and does NOT delete the DN.