Atrius97

Change the file extension yourself, or overwrite the original file you opened in PKHeX when you're saving your changes. 

It is not empty. Set your filters for species and OT Version correctly and hit "Search".

It doesn't display encounter templates without filters set, otherwise it would attempt to load every encounter for every species from every game all at once, that's potentially tens to hundreds of thousands of encounters.

This doesn't appear to be a PKHeX issue, I can't replicate this in-game.
Try Citra support, this is likely a texture glitch related to the emulator.

Use the encounter database under Tools > Data. Don't try to make Pokémon from scratch.

They have preset stats, as well as size values, nature, and Tera Type. If you don't know what the legitimate version looks like, you shouldn't be trying to fill in details by hand.

Why is a newly released Tera Raid event (or a mon bred from one) illegal on PKHeX/SysBot.NET?
The latest stable version cannot know about an event released after it. SysBot.NET only pulls the latest stable PKHeX.

Please note that the development build is not guaranteed to be compatible with PKHeX-Plugins or SysBot.NET, and we do not provide support for this use case. If you complain about problems due to updating to unstable versions, we will recommend you revert to stable.

Are you sure it's a legitimate cartridge? Restoring a clean savefile should have cleared the error, but bootleg carts would have issues both with reading and writing the savefile.

It's also possible the cart is legitimate, but damaged, in which case I'm unsure what can be done.

To my knowledge JKSV doesn't see NDS carts, you may want to try one of the other options:
https://projectpokemon.org/home/tutorials/save-editing/managing-nds-saves/
It's also possible that the savefile is beyond recovery.

Make sure that you're editing the file named "main", not the file named "backup".

You can obtain the files yourself by using the encounter database in PKHeX under Tools > Data to find those encounters, and using one of the PID mismatch guides to find a set of values where it can be shiny.

See below:

Assuming you're editing a Gen 8 or Gen 9 game, make sure you're making your changes in PKHeX to the file named "main", as that's the savefile the game loads when booted. The file named "backup" is the backup savefile loaded if the main file is corrupted.

In a lot of cases, an IV of 1 in Speed or Attack is also sufficient for competitive, it doesn't have to be exactly 0.

This is incorrect. The ribbon does not appear to be obtainable, despite being described as being granted randomly via Surprise Trade. PKHeX flagging it as illegal is accurate, because it IS illegal until proven otherwise. Similarly to the Item Finder mark, the developers appear to have forgotten to code any way for it to be granted ingame.

As I said, it seems unlikely to be enabled at all, even if the logic was intended to be server-side.

If the official guidebook claims the chance for it to be granted is 1/100, we should have seen thousands upon thousands of people reporting having obtained it. To date, no one has come forward with a legitimately obtained one, including several youtubers and streamers who personally performed thousands of Surprise Trades (a statistically significant amount, the chances of them not having obtained it at least once is astronomically low if it was actually enabled) without seeing it granted even once.

We've seen very, very few people claim to have found one, and all of the Pokémon that it has been seen on so far were very obviously hacked, so the ribbon was likely assigned by cheating before it was traded, not by the server during the trade.

No. While the official guidebook claims the chance for it to be obtained is 1/100 from Surprise Trade, no logic appears in the game to grant it, and players with tens of thousands of Surprise Trades performed haven't reported seeing it, ever.

It appears that GameFreak forgot to program a way for it to actually be obtained, along with the Item Finder Mark, which is similarly unobtainable.

Use the encounter database under Tools > Data if you're unsure of what is legal.
Alternatively, obtain a legitimate egg ingame, and look at it in PKHeX to see what values exist there.

See this guide:

See this reply for reference:

FAQ
Do I need EmuNAND for my Switch?
EmuNAND is only if you want to do potentially bannable things offline.  You do not need one if you are not doing bannable things. None of the projects here need to be run on EmuNAND, particularly if you want to go online, and we generally will not provide support for whatever you are doing on one.

Can I go online on EmuNAND?
This is not recommended even if you haven't done bannable things on it, especially if you've been online on SysNAND.  Uploading mismatched system logs to Nintendo, or clearing your system logs, is bannable.

Is it safer for me to edit in SysCFW and then boot in OFW?
These are the same partition. Editing in SysCFW writes to the same place that OFW boots from.  Bannable things are still bannable in OFW.  It can be slightly less safe to boot into OFW after SysCFW due to telemetry reasons, but bans have not been connected to this.

What if I already created an EmuNAND?
You can reformat to erase it and reclaim space, or simply ignore it and stick to using SysNAND. 

Information about Switch Bans and an explanation of how emuNAND is supposed to work:
https://nx.eiphax.tech/ban

Known Ban risks:

I can't replicate "nothing showing up" in the latest version of PKHeX. Here's the results for filtering for Ditto, Violet as the OT Version, and Static only. These 4 ditto are all 4 raid encounters "in a crystal cavern".

Make sure you're selecting your filters properly, and you're using the Encounter or Mystery Gift Databases. The "PKM database" is a separate feature.

The encounter database is already there. Set your filters and hit "Search" to have results appear.

This Primeape appears legal in the latest version of PKHeX. Please don't report issues with outdated versions of PKHeX.

Edit: I misread. I'm not sure whether this is an issue with PKHeX flagging it as legal when it's actually illegal, or if GameFreak has an issue with their whitelist.

Use the encounter database until Tools > Data instead of trying to make stuff from scratch. Additionally, Tera Raid pokemon have a PID that is correlated to their IV, HT/WT, EC, Nature, etc, which means their stats cannot be altered without recalculating the others via an RNG calculator such as Tera Finder:
https://github.com/Manu098vm/Tera-Finder/

The encounter you selected is a fixed symbol encounter, not a wild symbol encounter or Mass Outbreak encounter. Fixed symbol encounters cannot obtain marks, excluding size marks and marks that can be earned post-capture like Parnter or Gourmand. 

Select a different encounter from the encounter database, it has to be a standard symbol or Outbreak encounter to be permitted to have marks.

Yes. Eggs are already fully determined when obtained, so PKHeX can see if it contains a shiny. 
Also instead of asking this you could have just, opened your save in PKHeX and looked.

We are not currently permitting SV savefiles to be shared, because we are unsure if it's safe. Past games like Legends Arceus have had savefile verification for publicly uploaded saves and it may pose a ban risk.