Looks to me like somewhere along the way an update to endpoint manager must have removed a bunch of line key types.
I had recreated all of the phone config files to point to a new server, rebooted 40 phones mix of T46G and T48G and now all the prefix type line keys are not displayed on the phones and that line key type is not available in the template ?!!!
Here are the only line key types listed now
endpoint manager 18.104.22.168
phone firmware 22.214.171.124