Hi Jack,
HipChat Server configurations are managed with Chef, which will automatically override changes to the system's iptables on reboot, system upgrades, etc.
You can place executable scripts in the /home/admin/startup_scripts to persist modifications to the system, including changes to iptables. If you log into your HipChat Server command-line interface/terminal and navigate to that directory, you should see a readme file, as well as a few sample scripts, describing how to do so. One script is called "firewall_hole" and includes a sample of how to modify iptables.
Be sure to copy and rename any sample scripts you might want to use, modify them as you see fit, then set them as executable for them to run at the end of each Chef configuration run - just be sure they don't have a file extension and are set as executable.
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