Cdragowski

So I had never played Colosseum before and didn't realize how early you could start snagging Pokemon. I assumed there'd be a tutorial or something. SO I missed the Johto starter from the peon I battled in Phenac. Can't remember the name but it was the one w/Croconaw. I went into PKHeX, managed to generate a legitimate Croc and placed it in the PC. Upon loading the game again I noticed that "Snagged Pokemon" did not account for the Croconaw I generated and this concerned me as I read you need to have caught and purified all 48 shadow Pokemon as part of the criteria for catching Ho-Oh at Mt. Battle. My question is, does the game check total snagged Pokemon or total purified Pokemon for this criteria? I read all other shadow Pokemon I missed are obtainable again, but from what I've gathered the Johto starter you first battle is no longer obtainable if not caught in the Phenac peon battle. Will I have to start the game again? Thanks in advance.