If the CT is burned it will need replacing whether or not it's the primary issue (excuse the pun). CT's usually burn when they're left open circuit, when they're unshunted there's no secondary current which causes high primary excitation and runaway voltages in the secondary side so double check the secondary circuit and its connections. CT's are particularly dangerous when they're on-line so be careful, they can kill. The secondary side of a CT must never be in an open circuit condition and must never be disconnected when the primary side is on-line.