Figure I would try this one out. How did serge get back to Arni and what happend to Wazuki when they got there. It is said they escaped Chronopolis, however they were brought there by accident and didn't know it exsisted. They didn't know their way around The Sea of Eden, let alone be able to sucessful navigate back to El Nido/Arni. Then there is nothing mentioned about Wazuki after that except he turned into Lynx. No one seems to find it strange that one day his father disappeared/missing. No one seem to question if he died/left/going crazy or anything. Also the sea to sealed, and they only go tthere because, as I said, the storm. They couldn't exit the way the came.
Schala sent them off to Chronopolis, and beckoned Wazuki to bring Serge close to the flame to be healed, and hence he became the new arbiter.
As for getting back, Wazuki and Serge escaped Chronopolis once it got operational again. Schala probably finished the last part of the mission, sending Wazuki and Serge's boat out of the Sea of Eden (how else would they get past the coral), and from there Wazuki sailed Serge back to Arni.
From this point, it's pretty vague. Either Wazuki then left and came back in 1010AD to kill Serge, or that he lived with him until 1010AD, when finally FATE and the flame had corrupted his mind, and then he drowned Serge and went back to FATE.
Most likely Wazuki left once he got Serge back because Wazuki seemed to have become Lynx earlier and that would explain why Viper and Lynx have a tight relationship, besides the point that Lynx exists in both worlds.