Can’t answer definitively, but probably lost. It was thought recovered for a moment after the battle of Dodowa in 1826, but that proved not to be the case. To quote:
At around one in the afternoon, the severed heads of prominent and even royal Asantes were brought into the British camp. A great stir was caused when what was thought to be the skull of Sir Charles MacCarthy was discovered. Carried in a leopard skin cover, the skull was wrapped in paper covered with Arabic characters and a silk cloth. Ricketts reported that before the battle King Osei Yaw had poured rum on it and invoked it to cause all the heads of the whites to lie beside it on the battlefield. Delighted to have recovered MacCarthy’s skull, Lieutenant Colonel Purdon had it sent to England. Embarrassingly the skull proved not to be that of Charles MacCarthy at all, but that of the late King Osei Bonsu. His younger brother had taken it into battle with him in the hope that it would offset the effect of an omen that had warned the king not to launch the campaign.
From The Fall of the Asante Empire:* The Hundred Year War for Africa’s Gold Coast* by Robert B. Edgerton ( 1995, The Free Press imprint, Simon and Schuster ).
Given that it receives no further mention, that the British would have undoubtedly have wanted to recover it and that they would have almost certainly crowed loudly had they retrieved it ( as above ) - I’d say it ended up lost to history.