Though it did not seem as if TC-1289 knew of his split personality, he did seem to have managed to bypass his original clone programming, and was thus deemed to be a fully sentient being. This meant that the Rebel Alliance, and later the New Republic, considered him responsible for the actions he performed unlike the hordes of other stormtroopers, who were simply mindless drones.
Alliance High Command became worried when TC-1289 started to contact Rebel operatives using call signs and signals known only to Zyix K'xxt, as well as using mannerisms and speaking unlike other stormtroopers, which led them to believe he was not quite what he seemed. Additionally, one operative captured by TC-1289 swore that it was a rationally thinking being behind the mask, rather than a standard 'trooper; "Someone with a split personality." his report said, "One minute, a bootlicking toady; the other, an intellectual, charismatic gentleman."
Alliance operatives later discovered K'zzt's logs and, though their scientists disagreed over the finer points in it, they all agreed that it appeared as if he had transferred his mind, memories and skills included, into the unprogrammed clone before he killed his own body. Because of this High Command feared that, unless he was captured, Imperial security could become suspicious over the circumstances of K'zzt's death and, upon hearing of an eccentric stormtrooper colonel, they may reopen the case and discover the truth. Though they did not reveal in the 10,000 credit bounty they put up for TC-1289 that they thought that K'zzt was alive inside his body, they did inform other Rebel operatives.
Despite this reward, TC-1289 was still in Imperial service by the time of Grand Admiral Thrawn's campaign against the New Republic, and his last known location at that time was aboard the Star Destroyer Crusader in the Kala sector.