Yes- a ROM update is the same as a hard reset in that it deletes all your user files and programs and reverts the device to the 'factory' state of whichever ROM you are using.
Presumably CoPilot is on your storage card? It ought to be still present after the ROM update, but make sure you remove the card during the process. CoPilot uses a folder called 2577 to automatically reinstall when the card is inserted.
As you are keeping the same device, your CoPilot ID should remain the same, but to be sure you can run CoPilot and use the facility to deregister it from the device; once updated and reinstalled just run the activation again and it will be re-registered on the device.
And just to repeat my previous warning- make sure your Orbit is CID unlocked with HardSPL before attempting any ROM updates. Details
Here