Magus recalls the incident (as it originally happened) and we see them being dragged into separate gates. A villager recalls the incident as it happened this time around, and mentions them being dragged into the same gate.
Since Crono and Co. changed history, the timeline is rewritten and Melchoir wouldn't be protected by TTI. But Magus is protected because hes outside of the rewritten timeline. In other words, Magus remembers the incident as he describes it and Melchoir when you first meet him in the game would as well. But now Melchoir will remember the incident as the villager describes it. The gate must have sent them to different times, much like the gate in Magus's Castle sent 3 to 65,000,000BC and 1 to 12,000BC.
Actually, that gate would be Time Bastard in action, since in these new events, they weren't in the palace to be dragged into the gates that will sent them to the corresponding eras. I'm sure wherever Belthasar and Gaspar were hiding while all that happened, they too were dragged into black gates like the former two.
Melchior back in 1,000 A.D. will still not know of these new events since he too is like Magus, he only knows about the original events. All four time traveled when it originally happened, meaning they will always appear in those years (except Gaspar by being sent to the EoT will only be once) no matter what future changes are done.
I see the Compendium states that Janus and the gurus were sent to the DBT at the same time their counterparts time travelled. Time Bastard saves the series from the duplicate problem and such but I see a problem: If Crono and Co. change history so that person X no longer has the opportunity to time travel, why is Person X's time travel preserved? Lets say that Crono meets Joe in 1100AD and learns that Joe will be sucked into a black gate in his kitchen 1002AD June 1st 8:00pm. So, Crono goes and finds Joe at 7:55pm outside his house and starts a conversation to stall entrance into the kitchen. By what I'm reading here you guys are saying that at 8:00pm Joe will vanish in front of Crono because a counterpart who time travelled on a timeline that
was sent to the DBT did so at 8:00pm?
Crono A remembers Joe from 1100AD because his experiences are protected by TTI. His counterpart who until now has done everything the same way as Crono will reach 1100AD and not find Joe. Whenever Crono A time travelled to 990AD from 1100AD is when Crono B will go the the DBT. All I see is a perspective issue.
Crono A is preserved because he is outside of the affected timeline. He is what changes the future.
Crono B is not preserved and is sent to the DBT because he is inside the affected timeline. He is the future that is changed.
Joe A is NOT preserved because he is inside the the affected timeline. He is the future that is changed.
Joe B IS preserved because he is not in the affected timeline. He is what changes the future.
If Crono went back in time and threw a brick through Joe's window the day before Joe time travelled, would the new 1100AD Joe remember the incident? Yes. The old timeline was sent to the DBT so that when Crono returns to Joe he will find that this version remembers the brick.
Let's say Paul, a mischievous time traveller, met Crono and Marle in 1002AD. Paul is also from 1000AD but started his time travelling adventures "after" (referring to Time Error, so Paul would see the new 2300AD if he chose to go there) Crono had saved the world. Then he went back to 1000AD and slipped Marle something in her morning coffee so that she could NOT go to the fair and meet Crono. This means she can't time travel - but the Compendium holds that this drugged Marle will disappear the exact point of time that the original Marle time travelled, thus foiling Paul's plans.
really guys? c'mon