It's unknown whether the games that come out in the future will be able to run on 4.x system menu and software, however, the current 5.x roms are playable in the 4.x firmware in gateway mode, using their 2.0 software. The emuNand is kinda future proof because say a game comes out that needs 6.x to run, well you can already run gateway red card in GW 6.x so you should be able to run that game, and we shoudl be able to getget emunand working with system software above 6.x, so if a game needs a higher version, you should be able to emulate the newer version and play.
About OP's problem.. Why don't you just install a hardware nand flasher and flash your NAND.BIN that you backed up before you formatted your emunand?