I think it had something to do with the fact that they kept colliding with alternate universes in the Beltline (for instance, the Emishi who had lost an arm and MakubeX who tried to strangle Ginji), and that Amon who showed up just afterwards was another universe's Amon... who just sort of didn't die in that other universe?

Although Ginji's wish for the world he knew probably just brought back their universe's Amon. ...I wonder who has the chimera now, if anyone has it at all.