Been testing this for a while and figured that I should probably tell someone: Pkhex while editing the GameCube games garbles the Shadow Pokemon data and causes some really weird things to occur.
Attached are the save file I edited and the backup, untouched (I used some action Replay but other than that it's pretty clean.) After editing, the Tyranitar and the Quagsire in my team reverted to shadow pokemon randomly, however the number of purified shadow Pokemon remained the same.
Before Editing:
After Editing, not touching either of these specific Pokemon:
This has happened with my test of XD where I didn't even use Action Replay at all, where it glitches the shadow Pokemon list and causes some shadow pokemon when encountered to not register as a shadow making them impossible to catch as well as causing the gift togepi to not be a shadow upon obtaining it and have shadow moves while not being a shadow.
While the glitches have been mildly amusing for me, I can see them being an annoyance for others. Hopefully it's just user error though!
01-GC6E-pokemon_colosseum.gci
01-GC6E-pokemon_colosseum_backup.gci