Merging a new AirBEAM.reg file WILL cause the device to begin checking into the Relay Server to which the device the .REG file came from was checking in.  It will also cause other Agent Settings from the source device to be replicated onto the other device as well. While this approach will do what you were trying to do, it is not really a recommended practice.  There are a variety of MSP feartures, such as Agent check-in conditions, etc. which could cause this to only partially replicate the exact configuration of the device from which the .REG file was acquired.  In addition, the Package inventory of the device will likely not reflect its actual configuration, which could cause the device behavior to be at odds with the inventory reported by MSP and with its Policy Compliance as reported by MSP.

To recommend a fully supported procedure, I would need to know more about the situation you are trying to deal with.  Has the device lost contact with the Relay Server with which it is configured to check-in?  If the device can still contact its configured Relay Server, it might be better to use one of a variety of ways to cause the device to pull new configuration from that Relay Server.  If you use MSP mechanisms to affect the change then MSP will be aware of the change and can keep everything in sync.  If you make changes in an out-of-band was as you were proposing, then things could get confusing.