It's a good question. I personally have not used the ETW very much, besides just experimenting a couple of times. So I don't know if you can preserve the two backups somehow, perhaps just by restoring the newest one last.
I don't think you will have any issues being that you replaced the motherboard. Afaik the stuff that ETW is meant to restore is not really related to the hardware, but rather user account settings/documents and things like that.