I've been reading up on the Napoleonic era and I've found some conflicting information. One source says that he was fired on the spot at the battle of Wagram by the Emperor for leading his fleeing men and the other says that he handed in his resignation after his Saxon division had been slaughtered. Both of these stories sound believable, but only one can be the truth.
While Bernadotte's unauthorized retreat from Aderklaa was dangerous, after the fighting on the first day his force was dangerously reduced. One of his divisions, under Dupas, was held in reserve position and had apparently been ordered to act independently and remain in position by Napoleon. Without the support of that division, Bernadotte felt that he lacked the strength to hold, so he retreated.
After the battle, he handed in his resignation on the basis that Napoleon had endangered his command by ordering Dupas to remain behind the line.