On Centos Redhat 5. I was able to restart atd with /etc/init.d/atd restart. My running jobs were unaffected and my scheduled jobs survived the restart:
$ date
Mon Dec 12 16:41:07 GMT 2011
As root:
# /etc/init.d/atd restart
They are still in the atq:
$ atq
2 2011-12-12 16:37 = bobby
1 2011-12-12 16:36 = bobby
4 2011-12-12 17:00 a bobby
What OS are you using?
On Centos Redhat 5. I was able to restart atd with /etc/init.d/atd restart. My running jobs were unaffected and my scheduled jobs survived the restart:
As root:
They are still in the atq: