no reason to reboot except of course when I tried using the cgminer stop/start or restart commands they failed to work and generated an error so the only option was to reboot. which funnily enough worked.  and I understand why

of course actually what I should have done was
1 cd /etc/init.d
2 cgminer stop
3 cd /usr/bin
4 mv cgminer cgminer.bak
5 wget http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.0-140908/cgminer
6 chmod +x cgminer
7 cd /etc/init.d
8 cgminer start

or do it in 5 steps

 1. cd /usr/bin
 2. mv cgminer cgminer.bak
 3. wget http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.0-140908/cgminer
 4. chmod +x cgminer
 5. Reboot