Ok, if your stuff in is in /home/pi, is the Blynk jar file there too?
You can do as follows to create the script. It depends a bit on your OS, but I’m assuming you run Raspbian? Behind the command I’ll put in brackets what the command does, for your convenience 
Put the script on the server
cd /home/pi
hostname~ # ln -s server-0.17.x.jar server.jar {this makes a link to the current server jar file}
hostname~ # touch server.sh {this creates the script file}
hostname~ # chmod +x server.sh {this makes the script executable on Linux, as Costas mentions too}
hostname~ # nano server.sh {this executes the editor to put the script in}
So, with nano started, you can copy/paste the script to the server.sh file.
Now you need to edit your COMMAND var. For you it would be something like:
COMMAND="/prefer/full/path/here/to/java -jar /home/pi/server.jar -dataFolder
/data/folder/here" {of course with correct paths for data folder and java link. Java should be in your PATH variable, but I still like it to be the full path, just in case ;)
Now press CTRL-X to exit and Y to save the script.
Now you can run the script with the parameters:
hostname~ # ./server.sh start
That’s basically it to get it running. The next server upgrade you can download the new jar file and:
hostname~ # rm server.jar
hostname~ # ln -s new-server.jar server.jar
And run the script with the restart parameter 
From this you can see the server.jar is actually a link:
OpenELEC:~/blynk # ls -ltha
total 38738
drwxr-xr-x 14 root root 1.0K Aug 27 16:57 ..
drwxr-xr-x 5 root root 1.0K Aug 27 16:28 static
drwxr-xr-x 4 root root 1.0K Aug 27 16:27 .
lrwxrwxrwx 1 root root 17 Aug 27 16:27 server.jar -> server-0.17.2.jar
-rw-r--r-- 1 root root 13.7M Aug 27 16:27 server-0.17.2.jar
-rw-r--r-- 1 root root 12.5M Aug 10 06:52 server-0.17.0.jar