The problem is the members could be from either world, so the events associated could be either version (they could contradict each other llike Acacia Sgt said).
For example, Radius is the chief of Arni in home world. But a member from another world may see things differently, because in s/he's memory, Radius is a hermit during the time. Pirate Fargo may not have any idea on what the Grandslam is, he (and his crew) may not know Janice and Sneff. And if the crew live a different life, their families or the people they used to know may have been living a different life was well, causing chain effects.
Unless there's a priniple to weave their stories seamlessly together, like Mr Bekkler's plastic time theory. But that is definitely some sort of "rewrite".
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BTW, the new timeline is missing something. The whole adventure seems shorn off, because Serge woke up on the beach as if he had only passed out for several minutes.
It is perfectly OK if what Schala said about erasing their memory is true because in the new timeline there's no position for the adventure. If I was Kato, perhaps I would omit this part to avoid misunderstanding. Since the whole mess has never happened in the new timeline, it is safe to say Serge's time got rewound like what always happened to Kid.
Too bad, Kato jacked the ending a bit as if Serge still "remeber" something, hehe. Maybe that was just a dream like the Fort Dragonian one, but who knows.