Ah I forgot, the Species property is automatically remapped to national dex id, since it's not a normal species it just deletes it.
You can always hex edit the file I guess, maybe I can add a rawspecies property that doesn't do the remap. edit: added! https://github.com/kwsch/PKHeX/commit/71970b3332e0a28efb171b64ac00d88ace122424