There's a few different ways to update the server, but I prefer starting with a clean download of the server and then just moving my world and changed configs over. That way I know any files removed from the pack is also gone and all configs are reset to the default values from the pack.
These are the steps I use to update to a new version, you'll have to tweak it for your use, depending on which configs you change or which additional mods you installed:
I have the current version installed in a directory called "~/Direwolf20110_1.x.x" where x.x is the version of the modpack.
And I then create a symlink from that directory to "~/Direwolf20" - so that the symlink always points the latest version.
Where the instructions below refers to ../Direwolf20, that means to copy from the previous version.
1. Find latest Server zip from
https://www.feed-the-beast.com/projects/ftb-presents-direwolf20-1-10/files (Click on version, scroll down to additional files to find server and use in step 3)
2. mkdir Direwolf20110_1.x.x && cd Direwolf20110_1.x.x # Replace x.x with the new version you download
3. wget
https://www.feed-the-beast.com/projects/ftb-presents-direwolf20-1-10/files/2361696/download # Depends on which version you download
4. mv download FTBPresentsDirewolf20110Server_1.2.2.zip # Depends on which version you download
5. unzip FTBPresentsDirewolf20110Server_1.2.2.zip # Depends on which version you download
6. Copy files from previous version: # Include any additional configs you also need, these are the only ones we use
a. cp ../Direwolf20/settings-local.sh .
b. cp ../Direwolf20/server.properties .
c. cp ../Direwolf20/whitelist.json .
d. cp ../Direwolf20/eula.txt .
e. cp ../Direwolf20/mods/TickProfiler-1.10.2.jenkins.20.jar mods/ # These steps depends on which additional mods you've installed
f. cp ../Direwolf20/mods/SleepingBag-1.10.2-1.4.0.jar mods/
g. cp ../Direwolf20/mods/ShadowMC-1.10.2-3.6.0.jar mods/
7. Modify configs: # These are changes we made to the base direwolf pack's config
a. config/Morpheus.cfg # Change SleeperPerc=10
8. Backup old server and stop it, in server console, type:
a. /ftb backup start
b. stop
9. Copy world from old server
a. cp -a ../Direwolf20/world .
10. Start up new server to test it
a. chmod +x ServerStart.sh
b. ./ServerStart.sh
11. If everything is working ok, update symlink
a. cd ~
b. ln -s Direwolf20110_1.x.x Direwolf20
12. Optional cleanup, if you're confident everything running fine, save the last backup from the old directory and delete the old directory