Madbronine

11 minutes ago, Sabresite said:

For the sake of argument, lets say I wanted to go fully legit.  Could I wipe my savegame and be ok? Or would that count as changed data too?

Yes, Since you generate a new save and a new game sync id you will just have a clean slate.

With pokehex you can always check to be sure, I don't have the time right now but you can:
- Backup your save data
- Delete the save game, hold UP + B + X in the title screen
- Play like normal till you can use game sync
- Check if everything is fine

Honestly you wouldn't need to do all this but if you want to be 100% sure you have the tools do to so.
I just checked the Global link, my account is fine while it has both of my saves linked.

It seems GF has put in a check before the game sync occurs,
my last game sync on moon was 24th before the banwave and my sun was the 26th after the banwave.
The only reason not to go online now on affected saves would be to wait for a definitive answer on why people are getting banned.
Removing the irregularity from your save would then "evade" the ban.

12 minutes ago, AurelionColress said:

I also genned complete National Pokedex and got banned. Could you please check your Moon's Save Data? I want to see whether Pokemon not belong to Alola Dex will be registered. I doubt that what cause the problem is not The National Pokedex but Marshadow's Dex Data. Thank you!

I checked all for my pokedex entry in pkhex. So I have the full international dex filled with all entries.
GF probably checks for pokemon that are unobtainable as that is the most effective way of weeding out obvious hacks.
And it has the lowest chance of banning innocent players since they couldn't possibly access them unless they traded locally.

I'm just going to post my case here for some additional info. 

Moon = Banned - genned mons [legal], max items [all types], pokemon dex complete, max money, edited trainer location and pokefinder.

Sun   = not banned - genned Mons [legal], 999x all medicine and item slot items and max money.

It seems Pokedex is the main culprit here.
My friends who have genned mons from me or themselves are not banned either.

The bans are save/game sync only and only restrict you from playing in battle spot, rating battles and global missions.
As far as I know the pkhex rules state that you shouldn't be playing battlespot etc with genned mons anyway, so this ban barely matters.

I think I deserve the ban but hey it was for science, I wanted to check if getting the shiny charm through the achievement of filling the pokedex was different from just adding it in.

Quote

Someone here states that they were genning legit Pokemon and they were banned in the wave. Being specific, giving a few of their favorite legitly caught Pokémon perfect IVs and making them shiny.

My reason to believe that they got caught was probably making a tapu or any other shiny locked pokemon shiny and unlocking the dex entry.
Like I mentioned earlier only my save with full pokedex got banned. for example I edited my sun/moon demo greninja to be shiny on sun and it didn't get banned.