Unlike most of the 1993 Annual debut characters, Empyrean appeared earlier than X-Men Annual (2nd series) #2. According to archived data on shipping dates, his small cameo as "J.B. Chambers" in X-Men Unlimited #2 hit stores two weeks prior to the annual.
In the 1990's, Hardee's restaurant had a special Time Flyers promotion starring the X-Men, with accompanying comics. In these comics, Empyrean was ultimately cast back in time to the era of the dinosaurs. He hasn't appeared since, even in mass character round-ups like the Decimation and 198 lists, or the Initiative potential recruits from the Civil War: Battle Damage Report. Though unconfirmed, it seems Marvel might be treating the Hardees comics as canon.