Atrius97

I don't believe there's a full tutorial here, but we do have a basic one pinned in our discord help channel:

https://discord.gg/66PzPgD

https://discord.com/channels/343093766477053953/367479180398428170/1093948772926631980

They should only know that move by level-up if they're level 52 or above, otherwise it has to be an Egg move. None of the clones you mentioned are high enough level to have learned it via levelup, so if their details don't match up to one hatched from an egg, they cannot possibly learn the move.

TLDR, They either have to be level 52+, or have hatched from an egg to know Hydro Pump.

That is correctly illegal, PKHeX is working as intended, it is not "100% LEGAL". Why do you think your starter pokemon should have a move that is only learned via breeding, when it was never an egg/didn't hatch from an egg with parents that knew that move? Move legality is determined by the encounter details, not just "the species can learn it, so it's fine".

If a move is learned via breeding, it has to be learned via breeding, not by you editing it onto something that was never an egg.

I also can't replicate the Geodude issue at all, the one I caught ingame and the one from the encounter database both appear legal. Either you modified it to make it illegal, or you used glitches that changed some value. Please provide a pk2 file for it as well.

Editing the pokedex will not undo the event flags for having seen/caught a legendary. If you cannot locate the event flag/values needed to change, restore an older savefile backup from before you encountered them/before setting them roaming.

PKHeX stores old backups in the bak folder if you've edited your game before, and some emulators may have old savestate backups as well.

Installing custom firmware:
https://3ds.hacks.guide/

Extracting your savefile:
https://projectpokemon.org/home/tutorials/save-editing/managing-3ds-saves/

If you are unable to access game/firmware updates through Nintendo on the banned console, that means it's "superbanned" and cannot even access the CDN anymore. These bans are rare, most banned consoles cannot access the eshop or online services, but still receive basic support and updates.

No. HOME stores unique data for each pokemon for each game. By creating a BDSP origin pokemon in SWSH or Legends: Arceus, HOME already expects that pokemon to have passed through HOME, and it expects to have already stored game specific data for BDSP. 

Since it didn't actually originate in BDSP, HOME looks for that data and finds nothing. It may resolve the issue if deposited into BDSP, but as a rule of thumb, HOME should "see" a pokemon for the first time being deposited from the correct game. Try to generate BDSP stuff in BDSP, LA stuff in LA, and SWSH stuff in SWSH.

A : Don't use public savefiles for Scarlet and Violet, as it's likely the have savefile validation and it may put your account at risk.

B : Those kinds of mods are either actual game mods/cheats that you have active, or something else, because it should not be normally possible to have newly generated encounters on an unmodified game generate like that from just a savefile. Did you download any additional files other than a single savefile called "main"?

C : Try booting the game holding the L button. That should disable cheats, mods and overlays.

My issue was resolved using this converter, I had the same problem:

Shininess is not determined by PID in Gen 1 or Gen 2, it's determined by the IVs/DVs of the Pokémon. 
https://bulbapedia.bulbagarden.net/wiki/Shiny_Pokémon#Generation_II

The PID and EC would be determined randomly when transferred from Crystal to Pokémon Bank. If you intended to alter the EC, you would have to edit or generate it in a different game.

In earlier games, changing gender was as easy as changing a single flag. In newer games, there are dozens, hundreds, or thousands of values that would need to be changed for the character's gender to be swapped. Clothing, model, gender specific NPCs and event flags, etc.

You are welcome to try and document all the different values required, but it's probably faster to just restart the game with the correct gender, and give yourself some overpowered pokemon to speedrun the game to get back to where you were.

The servers have some restrictions on origin game version. The wondercard will not account for a gift redeemed on the wrong game version, but the servers may.

PKHeX will generally simulate official transfer methods, so it should simulate a trade.

You have to update Hekate AND Atmosphere to boot into custom firmware after an update that breaks both.
https://nh-server.github.io/switch-guide/extras/updating/

Do not try to directly overwrite or save the file to your SD card. Save/Export it to a location on your computer like your Desktop, then move/copy it to the correct location.

Are you sure it's a legitimate cart? Bootleg Gameboy carts often store the savefile differently than official carts, and that can result in bad or corrupt dumps.

If you purchased it way back during the original release, then ignore this, but if you purchased it used, it may be a bootleg.

You don't need a flashcart to get event pokemon. All you need is some kind of cart reader, or DS flashcart, to extract your savefile, and then you can insert the wondercard data directly into your savefile. 

https://projectpokemon.org/home/tutorials/save-editing/managing-gba-saves/
https://projectpokemon.org/home/files/file/645-mystery-gift-tool-gen-3/

If you're trying to open a box data bin file, it has to be for the correct game/generation. Opening a bin file for say, the box data of all the pokemon in Gen 7, in a Gen 4 game, will fail.

That aside, you don't have to import files at all. See the encounter database under Tools > Data, every possible encounter template is available there.

This appears to be a bug in the program, I've submitted a github issue on your behalf.
https://github.com/kwsch/PKHeX/issues/3834

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Actually PKHeX account for this too, a detection for this scenario is in the code.

It still gets caught on the static encounter check. You're welcome to try in the latest dev build, but I can confirm it doesn't currently account for this.

This is actually possible, but PKHeX doesn't account for it yet. VC Gen 1 transfers with the "wrong shiny stats" (swapped Attack and Defense), during Transporter v1.2, could wind up shiny and female on transfer, even if they had the 1 Female to 7 Males gender ratio. 

To my knowledge, this was corrected before the release of VC Gen 2, so this was only possible until Sept 5th 2017, with VC Gen 2 releasing on the 22nd later that month.

It's also a short list of species, the three Gen 1 Starters, Eevee, Fossils, and Snorlax.

This is a known issue, Pokémon that arrive via Pokémon Transporter may have no HT language and a strange HT memory.

This CAN happen legitimately, but currently PKHeX doesn't validate it, and it's a temporary issue anyway, as all HT values are rewritten any time the Pokémon is traded or transferred to a new savefile. You're safe to ignore the error, it will resolve on its own as you move the Pokémon between games.

Question, if you lost your physical copy of Shield, like the actual cart, but you still have the switch itself with the savefile data, why not just use Pokemon HOME to move it out of Shield?

Saves aren't stored on the physical cartridge anymore, so as long as you didn't delete/corrupt the save data, factory reset/break/lose the switch, your data is all still there.

You can even purchase another Shield cart and it will work as usual, with all your data intact.

Please do not repeatedly create new posts with the exact same question. The other two posts have been hidden. Post once and wait for a response.