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.