I got to about the 4th post in this thread and couldn't bear it anymore...
Here's MY theory on what happened. Marle travels back in time, the current "Timeline" still exists! It is not instantly changed! Marle is not INSTANTLY found on the mountain. Crono travels back in time, finds Marle in the castle, everyone THINKS she is "Leene". Leene is NOT dead YET, because she hasn't been found. Marle disappears because she does not exist in this timeline. At this point, yes, the present is changed, because at this point, they called off the search for Leene, which means she eventually dies, which is why Marle "disappears" in the first place in 600 A.D. In other words, the family line stops there, because Marle does not exist in 1000 A.D.
If you go back in time and kill someone's father, then their son doesn't exist in the "present". Its the same principle here, Leene is killed, therefore Marle does not exist, Marle does not replace Leene, because she disappears in 600 A.D. as I said. Also, if you travel back in time, that doesn't mean you don't exist in your time because your time HAS NOT HAPPENED YET!