Firstly locate your server on the home page of the panel
As you can see, my server software (pocketmine) is telling me that it is out of date
Next, Head to the management tab
Locate the server.properties file
Now, proceed to click the download button
Then, you would want to navigate to the System tab and press the reinstall button
It'll now prompt you if you were sure. This will not delete any of your worlds / plugins
Now find the server again and click on manage
Now, go to the management tab -> files Then, find the server.properties file
Now, upload the server.properties you downloaded earlier
Now you can start your server!
You can always change the server software file like the server.jar / Pocketmine.phar with a simple download from their release pages. Just make sure you download the right file.
Paper / Waterfall https://papermc.io/downloads
Spigot (Via buildtools) https://hub.spigotmc.org/jenkins/job/BuildTools/
Vanilla bedrock https://www.minecraft.net/en-us/download/server/bedrock (choose ubuntu)