1.NAND images are encrypted by console-unique keys and movable.sed.
You need to decrypt it totally before transfer to another of the same region, also old to old, new to new.
2.N3DS NATIVE_FIRM and O3DS NATIVE_FIRM have different TitleIDs, and there are other titles with the same issue.
To totally convert it you would need to alter the dbs - and for me at least, this is impossible for public known tools.
Fortunately you're talking about EmuNANDs, so that at least you would have almost no risk of bricking the SysNand for using EmuNand.