SLF, you appear to be still confused.
When the flight started, the Commander was in LHS as is usual, and the lesser experienced of the two FOs, Bonin, was in the RHS.
At 0200 the other (more experienced) FO, Robert, returned from his rest and took LHS seat in place of the Commander. The Commander appointed Bonin as Pilot in Command, notwithstanding his lesser experience, and Bonin continued as PF still in the RHS. The Commander left the cockpit and went for his rest.
When the Commander returned, he took neither LHS (his usual seat) nor RHS, but left both FOs where they already were. He was presumably in a jump seat, behind them, and not at the controls. Bonin, RHS, continued as PF. Robert was still PM. The Commander was calling from behind them.
If you want more, please read the threads first, like most of us have, instead of jumping to incorrect conclusions.