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We all know they made two movies because muh moniez, however here is an in-canon explanation as to how both versions were able to take place.
Pokémon White: Victini and Zekrom depicts the events as they occurred in the original timeline. In this timeline, Damon used the revival herb he obtained from Luis to revive Ash's brain, causing him not to lose to Cameron and and come in the top 4 like he has in previous leagues. As Reshiram had sided with Damon, it was sent to attack Ash at the start of his Unova journey, sending huge streams of fire out of the sky towards Pikachu. Although Pikachu was burned, it did not lose its electrical abilities and was able to kick Trip's ass with ease.
However when Ash and co. traveled back in time during the Arceus movie, they altered the balance of the timeline, causing certain events in the far future to be altered. The ideals of Reshiram and Zekrom became switched, resulting in the altered future of Zekrom siding with Damon and attacking Ash's Pikachu, causing it to lose to that Snivy. Because Damon now had a Zekrom, he used it to stop the heard of Bouffalant instead of Reshiram, resulting in Luisa giving him a Blitzle Charm instead of the Revival Herb he would have got from Luis. Because he did not have the Revival Herb, he was not able to use it to revive Ash's brain, causing Ash to lose to Cameron.
Basically, Pokémon White: Victini and Zekrom depicts the original series of events surround Damon and Victini, while Pokémon Black: Victini and Reshiram depicts the series of events as they occurred in the current timeline of the anime.
