Tente o comando timeout
da seguinte forma:
#!/bin/bash
echo "Starting Backup of Ubiquiti Radios"
while read one two; do
if timeout 60 sshpass -p 'supersecretpassword' scp -o StrictHostKeyChecking=no control@"$two":/tmp/system.cfg /mnt/hgfs/Ubiquiti/$one.cfg; then
echo "$one Success!"
else
echo "$one Failed"
fi
done < /usr/tmp/Script/Links.csv