This is a little outside my standard realm of topics but you never know who might need it. I run a Minecraft server and with the constant updates lately I've noted my process to make a little easier for me not to miss a step in the process. If it helps someone else out there, you're welcome.
I use the "screen" command to keep my server running. Whenever I need to update I need to kill the previous "screen" process first.
List server processes
From that list you'll be able to see your "screen" process, get the PID# and kill it.
kill #Screen PID#
Minecraft Server File
Delete the old "minecraft_server.jar" file since we won't be needing it anymore.
Download the updated "minecraft_server.jar" file from the server.
A New Screen
Open up a new "screen" instance.
Start the server back up within "screen".
java -Xmx1024M -Xms1024M -jar minecraft_server.jar nogui
Leave the "screen" instance without exiting it by "detaching" it from the current terminal window.