My exact procedure was as follows, all on an old 3DS XL (games and NNID were installed, I did not unlink the NNID before the procedure):
- Made a full SD card backup
- Downgraded from 10.3 to 9.2
- Used emunand9 to dump the sysNAND
- Used emunand9 to format the emuNAND partition on my SD card using the sysNAND as the source (not the backup, though this shouldn't matter)
- Did a system format using the system settings menu on the sysNAND to unlink the NANDs
- Restored the SD card backup
- Updated emuNAND using the system settings menu
At this point, everything worked insofar that I had all of my games and data on the emuNAND. Upon trying to open the eshop, however, I received an error (022-2634). This error would repeat whenever I would try to access anything requiring an NNID login, such as system transfer, NNID settings, and the aforementioned eshop. A quick goolgle search lead me to a thread on this site explaining that this happened after formatting the sysNAND while the NNID was attached to both the sys and emuNANDs. That's what lead me to try the convoluted solution I mentioned earlier, which fixed the issue.
Now, this is just speculation, but it seems that if an NNID is attached to the sysNAND to begin with, you go through the whole emuNAND creation procedure, and you format the sysNAND, the 3DS or the online services believe that your NNID is no longer linked to the 3DS. So, when you try to log in or use one of the services I previously mentioned, you get an error.
I have no idea if there's a better way to prevent this from happening besides making sure that there is no NNID attached to the sysNAND to start with (impossible unless you format the system), or you format both sysNAND and emuNAND after you're finished with the setup. I also don't know if this is even a problem other folks are having, but I did run into it on two separate systems.