We understand how the Pokédex male/female/shiny works, but I don't know how special forms work. I think that Suloku made some research about this.
I know exactly how it works, I documented it in projectpokemon (for some reason the page is down now).
It's actually easy to implement once you know how it works, it's just that it hasn't been implemented in pkhex or phbank yet. Also, I think I mentioned it already, but on ORAS, there's the "dexnav level" variable for each pokemon, which should be set to at least 1 if the pokemon has been encountered, which of course includes having owned the pokemon, and thus phbank should be setting it to 1 if it is 0.
EDIT2: I just checked github, I think Gocario already added dexnav level updating when setting new pokemon on ORAS.
And why would you want to clear form data?
EDIT: OK, you want to delete eternal floette's data. I hoped this would have been added to pkhex by now. I don't really have the time to code an app that could modify the "form dex" as I call it, but you can still delete it manually. projecto pokemon is down right now, so as I don't remember the offset at which formdex starts I can't give you propper instructions. Tell me via pm when it is up again and I'll tell you how to, or if you are afraid to hex edit, send me your save trough pm when pp is up again.
I think maybe we can use transporter access to make ds save manager that run over transporter (like with xml file and poke transporter title)
No, that won't work. I think poketransporter and dream radar use some raw read/write functions that aren't implemented in ctrulib. They are 3ds apps, so they have 3ds savegame, they access nds by directly accessing the slot, they way we are reading 3ds saves is trough nintendo's functions made for that purpose, since 3ds game and apps have a filesystem for savedata, while NDS are just plain read/write memory, no filesystem at all.
Or that's what I think at least, I might be totally wrong, there's just not that much interest in reading nds cartridges from 3ds mode since you can't do anything exiting (except save managing and rom dumping, which for me is exiting enough, but well).