Pokémon disappearing in PC & inconsistent Saves

[VictorV111]

Scenario 1:

In Pokémon Soulsilver I caught 2 Vulpix and engaged in a few Trainer Battles.

I open the Save in PKHex.

The Vulpix appears as "caught" in the Pokédex; The XP gained from Trainer Battles is there; Both Vulpix do not appear in PKHex.

Scenario 2:

In Pokémon Soulsilver I caught 3 Magnemite.

I open the Save in PKHex.

They appear there normally. I edit 1 into Magneton. I edit 1 into Magnezone. Legality check: Tick.

I export the Main.

I open the Game: 3 Magnemite in their original Position. No edits carried over.

 

(In short: sometimes Game Pokémon dissappear in PKHex; Sometimes PKHex Pokémon disappear in the Game)

(This Save will only have the Scenario 1 - Vulpix Error)

Pokémon - SoulSilver.sav2 (The Trainers in the South haven't been battled, because I gave myself the Gym Badges. If I went through the entire Region again, I would have to do everything again, once the error occurs again.)

Attempted Fix: Starting a new Game, editing TID, SID, Items etc. too look as close as the old file. Initially works. No Game-PKHex problems. But after 2-3 Saves, this problem comes up again.

Edited April 10, 2020 by VictorV111