I believe there's actually another incident in between the ending of Immortal Regis and Cavalier of the Abyss that caused Nex to lock Serin up. Even if Nex is the savior they wouldn't have let him lock Serin up immediately. He'd have needed to gain political support and entrench himself as the Regis first. Not to mention Serin had his kids, so there must have been a lot more story that was not told in between.
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