Briefly:
cd /usr/local/FlashphonerWebCallServer/bin
./shutdown.sh
./startup.sh
With diagnostic commands:
1) cd /usr/local/FlashphonerWebCallServer/bin
2) ./shutdown.sh
#Just to be sure that Flashphoner process is properly stopped
3) ps aux | grep Flashphoner
4) ./startup.sh
#Make sure the server is restarted and logs are
5) tail -f /usr/local/FlashphonerWebCallServer/logs/flashphoner.log
#Make sure the Flashphoner process is alive.
6) ps aux | grep Flashphoner
Steps 3,5,6 are optional.