Well, Magus may have forgotten those memories, or perhaps he does possess them moments after history is after history is changed and Crono and Co. meet with the child wizard? Just a thought, as time seems like an instantaneous thing in the CT realm.
V Translanka is right. Time travelers are protected from any changes made to their past world line. Any time travling event creates a new, separate timeline, and the original timeline is discarded into the Darkness Beyond Time. The time travelers themselves are unaffected by these changes because the act of time traveling comepletely separates them from the causality of original timeline.
Magus originated from, and bears the memories of the original timeline where Crono never traveled through time. By time traveling, Magus and the others created a new timeline where the events of 12000 BC occured differently. In this new timeline, a new version of Janus existed who has no relation to the original version of Magus.
Magus cannot have any memories of what the new Janus experienced, but the adult Magus can sense the Black Wind as well. If Crono was fated to die, then it would have been plainly visible to Magus.
