PokéBase - Pokémon Q&A
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This is a very unique problem that I've been having. I've tried looking up things on other sites, but nobody seems to be having the same problem or knows what the problem is.

First of all, I must clarify that I have been to Pal Park. I have beaten the Pokemon League multiple times, defeated all eight Pokemon gyms, and beaten Red. I have also successfully transferred from LeafGreen version before.

Here's the problem: Whenever I try to migrate from Ruby/Emerald/Sapphire, the option doesn't appear. In addition, when I open Ruby/Emerald/Sapphire after the unsuccessful migration, this message appears: "The saved file has been corrupted. The game cannot be played." I am then given an option for a new game, thus loosing all of my current progress and Pokemon.

Additional information: I'm not sure if this has anything to do with the problem, but my LeafGreen version was new when I bought it. The other three were pre-owned. Also, if I try to play any sort of DS game while one of the three non-migratable cartridges is in, the same corruption message appears and my saved file is deleted. Can anyone give me some official information on this?

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Well, it obviously has something to do with those cartridges. Being pr-owned, something might have happened to them when they were in the possession of the previous owner? Do you ever have any problems playing the games that sem peculiar?
This happened to me
I believe your RSE could be a bootleg.
I don't think the DS versions had bootlegs though, so having them pre-owned probably means they're still originals.

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Something must be wrong with the cartridges, plus I've experienced this before. My sapphire worked fine when I transferred Pokemon. But when I went onto sapphire to get Pokemon ready for transfer, the save file was corrupted. I ignored that and tried to transfer some other Pokemon to my pearl version. The sapphire thing did not show up. So I guess the state of the GBA game is what "determines" the thing appearing. I hope you get what I'm saying. Hopefully this answers your question. Hope I helped!(ish)
Source: experience

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