@extide:
Depends on how the rules are created, if they are generic rules then they don't apply to any specific interface. If they are bound to an interface it would be the friendly name like LAN or WAN or OPT1, etc, not the freebsd name like em0.
I would say just export your config, build the new box, import the config and then see where you stand. You should be pretty much ready to go, you will just need to reconfigure the interfaces themselves, but the rules should be fine.
Awesome! Thank you very much for clearing that up. Knowing that it may not be a waste of time makes me a little more comfortable bringing down the network to attempt this. I'm going to give it a go.