PID Mismatch - Origin Game RSEFRLG (Pokefinder) - Using PKHeX

This guide to resolve any issues users get when they try to change nature or PID of a Pokémon from Gen 3 or Gen 4.
DO NOT USE ANY POKéMON WITH MODIFIED PID ONLINE!

Foreword
The reason why people get various PID-Mismatch or Invalid Encounter type of messages, is because they did not modify the Pokémon correctly.

In Generations 3 and 4, due to an in-depth understanding of how the Pseudo-Random Number Generator works (as well as game mechanics), the Personality Value (PID) is tied to various other values related to the Pokémon generation procedure in-game, such as Individual Values (IVs), Gender, Ability slot, Nature, and Encounter Slot. (Encounter slot refers to the programmed data in a table, that hosts a list of level and species that can be encountered in a map)

TL;DR: Due to how RNG is called, PID, IVs, Nature, Gender, Ability, Encounter slot are related and can be derived.

Basic Preparation
1. Pokefinder will be the tool we use to find correct information (PID/IVs etc)
2. Time and patience. I cannot stress this enough.
3. Know whether the specific Pokémon is Stationary/Gift or Grass/Cave/Surfing/Fishing/Rock Smash wild encounters.
4. Begin with 'priority of information' in mind. Which is more important: PID or IVs? That will be your starting point.
This will be basis for choosing Search via PID or Search via IVs below.

Note: Do know that there are scenarios where the PID or IVs you want would be impossible. Learn to adapt to such scenarios.

5. If you're trying to make a shiny, and TID/SID isn't all that important to you, ignore shininess for now.
(There's a Shinification portion further down. Run through the regular steps first)

Search via PID - Stationary/Gift

Spoiler

Before we begin: All Stationary/Gift in RSEFRLG uses Method 1.

Let's say for this example, we're trying to fix Deoxys caught in FRLGE

1. Launch Pokefinder > Gen 3 Tools > PID to IVs

2. Paste the PID shown in PKHeX into the textbox, hit generate. Then, choose a PID from Method 1

3. Copy the IVs into PKHeX

Search via PID - Wild Encounters

Spoiler

Before we begin: Wild Encounters in RSEFRLG uses Method H1, H2 or H4. They are basically groups that contain an assortment of Method 1, Method 2 and Method 4.

Keep in mind the Synchronize and Cute Charm mechanics were only introduced in Emerald.

Let's say for this example, we're trying to fix this Clefairy caught in FRLG.

1. Launch Pokefinder > Gen 3 Tools > PID to IVs

2. Paste the PID shown in PKHeX into the textbox, hit generate. Between Method 1, 2 and 4, choose the IVs you like best.
Keep a mental note that what you chose might not necessarily work, and you'll have to come back to this step if it doesn't.

In this example, I'll be sticking to Method 1

3. While keeping PID to IV window open, go back to main window, click on Gen 3 - Wild

4. Select intended game as profile. If you don't have a profile, set up a simple one.
Since this example is based on Clefairy in FRLG, that'll be my chosen game.

5. Select Searcher, select Method (if unsure, go with Method H1 for now), Input Encounter type and Location (refer to PKHeX), Input IVs (refer to PID to IV), then hit Search.
If you're not searching for Emerald, Lead has to be None.

Note: Make sure you select correct encounter types too:

Also: Cave encounters uses the same procedure as Grass encounters.

6. Check if the PID generated and the Met Level given is the same as the one on your Pokémon (or the Level you decided on)
Met level only applies if on Generation 3 save. If it's been transferred up, Met level changes.

Two things you can do if the Level differs:
a. Modify the Met Level on your Pokémon
b. Cycle through Location (if it's in a cave system where Encounter Rate changes at every level)
c. Cycle through Method H1, H2 and H3 and repeat Step 5.

If you go through (b) and (c), and you still cannot get the desired PID, it's likely this PID/IV/level combo is not possible to encounter for this Pokémon at the selected location. Go back to Step 2, select a different one.

7. If PID and level matches, simply modify your Pokémon with the correct stats generated, such as IVs.

Search via IVs - Stationary/Gift

Spoiler

Before we begin: All Stationary/Gift in RSEFRLG uses Method 1.

Example: I want to modify a Deoxys captured in FLRGE to be Flawless/Near Flawless IVs, but I do not know what the PID should have.

1. Pokefinder > Gen 3 - Stationary

2. Select Searcher, Method 1, input wanted IVs, Search.

3. Note: Not every Nature can have Flawless IVs.
If no results appear, double-check that you're in Searcher tab.
Also, give the IVs a bit of range if no results appear.

4. If results appear, input the PID, IVs and Nature into PKHeX

5. When relevant fields are modified correctly, it'll become legal

Search via IVs - Wild Encounters

Spoiler

Example: I want to modify a captured (not bred) Clefairy to be Flawless/Near Flawless IVs, but I do not know what the PID should have.

1. Gen 3 > Wild

2. Select intended game as profile. If you don't have a profile, set up a simple one.
Since this example is based on Clefairy in FRLG, that'll be my chosen game.

3. Select Searcher, select Method (if unsure, go with Method H1 for now), Input Encounter type and Location (refer to PKHeX), Input IVs (refer to PID to IV), then hit Search.
If you're not searching for Emerald, Lead has to be None.

Allow some range for IVs, cause not every encounter and location allows for Flawless IVs.

4. If no entries appear, repeat Step 3, cycle through Method H1 to Method H4.
If still no entries appear, broaden your search criteria (allow wider range for IVs, for example)

5. When an entry shows up, copy the relevant information into PKHeX

6. When all information is inputted correctly, it'll be legal

Note: For Unown, given that the PID generated is XXXX0000,
you'll have to paste it as 0000XXXX in PKHeX.

(Alternatively, use Pokefinder > Gen 3 - Stationary and search using Reverse Method 1)

Shinification

Spoiler

There's 2 ways to make a Pokémon shiny:
a. When Search via IVs (for shiny PID), input the intended TID/SID and select Shiny Only

This method isn't perfect, as not every PID/IV/Nature combo would result in a shiny Pokémon for the particular chosen TID/SID combo

b. After obtaining wanted PID/IV/Nature combo, use the PID to find shiny TID/SID combo.
Using this Deoxys as an example:

B1. Pokefinder > Gen 3 - IDs

B2. Select the tab for the relevant game. In this example, it'll be FRLGE.
Paste in the PID, and select TID (can be wanted PID or random PID), then hit Search