He can't tempt Bohemian and Hungarian elites by offering a Crown to one and more titles/priviledges to the others?
IOTL, Nappy tried persuading Nicholas II Esterhazy, a prominent Hungarian noble and supplier of soldiers for the Habsburg cause, with an offer of a Hungarian crown, but even after the crushing Habsburg defeat at the Battle of Wagram in 1809, Esterhazy fervently declined. His loyalty to Vienna helped preserve the empire's bargaining position, to an extent.
I'm afraid a better way of creating a free Hungary in the midst of the Napoleonic Wars would be through Tsar Alexander of Russia being a closer friend of Napoleon and committing further to the 1809 campaign against Austrian Galicia-Lodomeria instead of just making small border adjustments, thus forcing the Habsburg Empire into a defensive strategy in an 1809 war and making independence a more palatable option for the Hungarian elites.