I'm not sure if I've wrapped my mind around this one completely yet, so bare with me on this (i'm kinda confused myself)...
Magus is thrown back to 12000BC after Crono & Company disrupt his "summoning" of Lavos, right? In the original timeline he was killed because he wasn't disrupted, right?
Welly well Wellerson the Third...
He then persuades the Queen (his mother, Zeal) that he is a great and powerful Prophet due to his knowledge of that time & place. Upon doing so, he tells her to lock up Melchoir (where are the other Gurus? killed? locked up as well?). In the original timeline this doesn't happen, and the Gurus are sent through time to various points, Gasper to the End of Time, Belthasar to some time around 2300AD, and Melchior to some time around 1000AD.
Now here's the tricky part. Since he was locked up (and then freed by Crono & Co), he never went to the Ocean Palace (instead he gives Crono the Red Knife and he sticks around the Earthbound Village.
So then the Gurus are never sent to those timelines, right? Heck, we don't even see him send JANUS forward in time!
So then, would all of that be paradoxed? Or is it shrugged off because originally they too became time travelers and are thusly not effected by the changes? At the very least, we have what the hell happens to all of them that aren't sent through portals in this new timeline, right?