I'm afraid not. I have the same problem. I did a system transfer emuNAND to emuNAND and I cant play my legit Four Swords Anniversary and also not my Ambassador GBA games on my New 3DS. There was a workaround for DSi games that made it possible to download them to emuNAND and make them playable in sysNAND, but this required linked NANDs, which is after a system transfer obviously not the case.
Yes, as I already said in my post. I have an Ambassador 3DS on 4.5 with emuNAND 9.5 and a New 3DS on 9.0 with emuNAND 9.5. I did a system transfer emuNAND to emuNAND. Before doing it a took an image of my SD card, this way I could restore my emuNAND on my O3DS pretty easy. Of yourse GBA and DSi still works in the sysNAND of my O3DS but as I already mentioned not on my emuNAND of my new3DS.