Like transferring Ambassador status to emunand? Yeah, that will work. You are just cloning the system's nand and reading it off the SD card instead so everything is exactly the same (but optionally updated to latest FW) as far as the system is concerned.
If you meant doing a system transfer to a new system? Then Ambassador status is carried over to the new 3DS unit. (I've done it before a few times. RIP my original Aqua 3DS)
I was more worried recovery if anything happens to emunand.