That really depends on how safe you want to be. I personally have loaded CFW on sysnand for backing up my legit sword save, moved all my legitimate pokemon to HOMe, then reloaded the save essentially cloning them. I might get hit with the next ban wave, who knows. It worked when HOME launched and here I am a little over two months later not banned yet.
As said, it is a risk I was willing to take to send those pokemon to HOME but keep them on my sword save. You could do the same by backing up your legit save, loading your "cfw switch file" on sysnand, reboot stock, go online send the pokemon to HOME, go offline, load cfw on sysnand and restore your legit save. As stated, this would slightly increase your ban risk. How much? I wouldn't know as I don't personally use emunand and just CFW on sysnand. I have been for a year and my switch isn't banned, yet. I accept this risk, you may not, but it is an option.