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Like how in gen 4 the second time you battle them some of them have Pokemon from other regions.

What games have this, and what are the differences from the first time.e to the second.

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Nobody in the DPPt Pokemon League uses Pokemon from outside of Sinnoh. I don't know what you're talking about.
i meant gen four (hgss) sorry

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In FRLG, after you complete the Sevii Islands quest, Lorelei has a Piloswine, Bruno evolves his two Onix to Steelix, Agatha evolves Golbat to Crobat and replaces Haunter with Misdreavus, and Lance evolves one Dragonair and replaces the other one with Kingdra.

In HGSS, after you get all 16 badges and beat Blue, Will gets a Bronzong, replaces Exeggutor with Grumpig, and replaces his second Xatu with Gardevoir. Koga replaces Ariados with Skuntank, receives a Toxicroak, and replaces Forretress with Swalot. Bruno replaces Onix with Hariyama, and receives a Lucario. Karen evolves Murkrow to Honchkrow, receives a Weavile, replaces Vileplume with Spiritomb, and replaces Gengar with Absol.

In ORAS, Sidney replaces Mightyena with Scrafty, replaces Cacturne with Zoroark, receives Mandibuzz, and gets access to Mega Absol. Phoebe replaces Dusclops with Mismagius, receives Drifblim, replaces one of the Banettes with Chandelure, and gets access to Mega Sableye. Glacia replaces one of her Glalies with Abomasnow, replaces one of the Froslass for Beartic, receives a Vanilluxe, and gets access to Mega Glalie. Drake replaces one of the Flygons with Dragalge, receives Haxorus, and gets access to Mega Salamence.

In BW, Shauntal receives Drifblim and Froslass, Marshal receives Breloom and Toxicroak, Grimsley receives Sharpedo and Drapion, and Caitlin receives Bronzong and Metagross.

In B2W2, Shauntal receives Froslass and Mismagius, (Gengar was replaced by Banette and Shauntal received Froslass on Challenge Mode) Marshal receives Medicham and Lucario, (Medicham is replaced Machamp on Challenge Mode) Grimsley receives Honchkrow and Houndoom, (On Challenge Mode, Absol is replaced with Honchkrow, Liepard is replaced with Tyranitar, and Grimsley receives Houndoom) and Caitlin receives Gallade and Metagross. (On Challenge Mode, Caitlin receives Alakazam, and replaces Sigilyph with Gallade)

Hope this helped!

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I don't think this is right.
In FRLG, they will only have different Pokemon on the second battle if the second battle was after the Sevii Islands quest. If battled twice before completing that quest, then their Pokemon will stay the same.
In HGSS, they will only have different Pokemon on the second battle if the second battle was after defeating Blue. If battled twice before defeating Blue, then their Pokemon will stay the same.
In RSE and DPPt, I don't think you understood what "second battle" meant. I'm pretty sure "second battle" is when a player challenges the Pokemon League after defeating them once earlier IN THE SAME SAVE FILE. Sidney doesn't change his RS team to his E team after being defeated once in RS, nor can RS and E load one save file.
oops, I'll edit it.
Better?
I think it's okay now.