thanks atledenin but that error only came up after the miner rebooted so the ssh connection was lost. I did rename the cgminer file back but the miner didnt start mining again. I ended up having to reflash back to factory settings and inputting my details in again. oh well at least it's mining again 
but with old cgminer 
but with old cgminer You just missed a step is all. Step 4 below. After you use wget to download cgminer, you have to change the permissions to allow execute. The permission denied error is because there is no permission to execute the command.
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
no need to reboot the device
/etc/init.d/cgminer restart
or
/etc/init.d/cgminer stop
/etc/init.d/cgminer start
rebooting gains you nothing except not understanding what you are doing.
all u r doing in this process is replacing a single file that is presently running, so simply telling it to stop the old one and start the new one is all that is needed... u r not changing or modifying anything OS related to need a reboot.
just like u dont need to reboot when changing frequency...