Ok. Basically there's no a difference between SysNand and EmuNand, both are functional NAND copies of your system internal memory. Long ago was mandatory to use an EmuNand to avoid system errors or bricks, now it's not necessary ever more (if you are using activelly an EmuNand is so easy and safe to inject/move it to SysNand, and just stand with an unique NAND).
And about the differences of both NAND type system versions, there's no really problem. You can always update to the latest actual version having Luma CFW updated. Then, the "downgrade effect" present on the process of moving EmuNand to SysNand is not a trascendental problem at all, it's just and "accident" if you will
The only annoying really thing is to have to install the homebrew set again
PS: I'm so sorry with you, because I don't speak/understand english very well. For this reason, perharps my explanations aren't no so good and the delays on my answers are evident
But I hope it helps and you can understand it