Originally, Xorn was intended to be a ruse, a false identity assumed by Magneto as explained in New X-Men (1st series) #146. Magneto was then decapitated in #150. However, #157 and Excalibur (3rd series) #1-2 revealed that (1) Magneto was still alive and (2) he wasn't Xorn. A second Xorn appeared, Shen Xorn, claiming to be the twin brother of the first Xorn, Quan-Yin Xorn, who had only believed he was / posed as Magneto.
In New Avengers (1st series) #16-20, the sum total of all mutant power energy removed from Earth on M-Day became a semi-sentient entity known as the Collective. Xorn's power signature was detected in the Collective in #18, and he was revealed as the guiding intelligence behind the energy field in #20. This implied that Xorn was not killed in #150 (indeed, if that Magneto was truly Xorn, then decapitation likely wouldn't work on someone who didn't have a head in the first place).