PokéBase - Pokémon Q&A
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It was in my box and just...............disappeared.
How did this happen? This was a clone in case this affects it.

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You come up with some really inventive tags IAS!!
How about let's NOT make inventive tags that are absolutely pointless.
True they were pointless but tags like battle-spot-hates-me make me laugh :-)

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I've heard of things like this happening...
Here's my theory, yet I have no real proof because I don't have the games code.
When you clone a Pokemon, the Pokemon cloned over the original will replace it's data over the one replaced. But if there is an error, let us say not enough of the data was replaced. The game will therefore say ''well this thing has no understandable code! it's all scrambled!'' and read the Pokemon as not existent as a Pokemon so the game will not allow you to see it in the pc. It probably does exist in your pc as random code.

Also when the cloned Pokemon deletes and replaces the data of the original there is a chance that when you stopped the trading/Cloning process you deleted it at the exact moment between the delete at replacement process of the pc sprite (before it was replaced, yet after it was deleted.)

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Someone else cloned it for me and I had it for 2 months.
Was it a clone of a clone?