It is by default in the /var/lib/pufferd/servers folder. In there is a json file, which contains the info on how a server (including the arguments) are set. Update that, then restart pufferd to apply it.
You can create and install a server using the Minecaft Forge template (make sure the Version and Memory (MB) fields matches what your modpack uses if possible)
Then, copy your modded files into the new server using SFTP (overwrite/replace the old files)
And lastly, rename the JAR you want to use to server.jar (If there's already a server.jar that wasn't part of your modpack, rename the old server.jar to something else like server.jar.old)
Most modpacks have their own server.properties, so the port and address you specified while installing may not be the same as the server's server.properties.
The authtoken in /etc/pufferd/config.json is not valid anymore.
You will have to log into your database and use the following to get the new token:
USE pufferpanel; SELECT name, daemon_secret FROM nodes;
Update the config with the new token, then use systemctl reload pufferd to apply the change.
Multiple weird and fun things happened on this trip!
1! For some reason or another, apache refused to acknowledge the existence of index.php at my initial pufferpanel install location (which was not /srv/pufferpanell). after installing at /srv/pufferpanel however, and changing the hosts file, voila, it would recognize it! (and therefore stop sending the 404 errors. apache was looking for /index.html and refused to go any further) But alas, now pufferpanel was throwing a 500 error! Aaah! Long story short, the pufferpanel mysql database and user never got made. as soon as those were made, everything worked fine.
Thanks to Nebcore/Disconsented for being super helpful in the discord, and bearing with me as I stumbled through everything.