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GS cloning and the Johto Pokédex

VeggiePopper

Doc Octillery FTW
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Hi everyone!!! You may not believe it, but back in the old days I never used the cloning glitch in my Gold version, but today I replaced the battery and started a new Johto Journey (anime dixit, LOL). I did the cloning glitch at the begining in order to have the three starters.
It did well, but later, when I received my Pokédex from Prof. Oak and saved my game, the save screen read:

"Pokédex: 1"


The Pokémon I caught before weren't added to my Pokédex! Not only they don't appear as caught, they didn't appear as seen. So it says I only have a Chikorita (the last Pokémon I picked); Cyndaquil only appeared as seen after I defeated James (the name I gave to Silver), and my Totodile seems like it doesn't even exist (WTF?!) despite me having it in my party =O; so it looks like I'll need to breed my starters to hatch new babies and register them in my Dex when they're born if I want it to be complete...

My question is, did it ever happened to you or something went wrong when I did the trick?
 
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