Not him, but his paternal half-brother of the same name who was born in
the early 1240s to their father's second wife, Isabelle de Courtenay.
The footnote cited does not say or imply "either" this Jean or his
father, but rather explicitly states that it most probably refers to
this Jean, whose father was his namesake ("sans doute Jean de Chalon,
comte d'Auxerre du chef de sa femme, fils de Jean le Sage, dernier comte
de Chalon"). The father Jean was count of Chalon, the son Jean was count
of Auxerre by his second marriage, to Alix of Burgundy.
Peter Stewart