Okay, I understand. It's the original Melchior who always arrive in 1000AD, every 1000 AD.
So Magus is not the only one who remember the original incident, and his case is not special.
That's pretty much it, though there is one difference: The Magus we have in our party recalls all of the incidents the way they happened the first time around, including no memories of the Black Omen existing in 600AD. Melchior/Belthasar/Gaspar, the way we knew them when we first met them, are not the same. They will always recall the Black Omen existing in their respective time periods.
So, we always see Magus A1, not Magus A2.
But we see Melchior/Belthasar/Gaspar A2 - because their gates open after the world has changed. Their "A1" counterparts aren't TB'ed, they are just sent to the DBT with the rest of the timeline where the Black Omen never existed/other changes.
All "B" counterparts are TB'ed, of course.
How do you figure? During the course of Chrono Trigger, we meet all A1 versions of the Gurus. When you first start the game and are collecting Silver Points, Melchior A1 is hanging out in Leene Square. When you first see Belthasar programming Poyozo Dolls, that's Belthasar A1. The first time you go to the End of Time, you meet Gaspar A1. The Black Omen is not yet present in any of these time periods.
Once you go back in time to 12000 BC, you meet Melchior B1 there, and could meet Gaspar B1 and Belthasar B1 as well, though we don't see them. You're correct that all the B1 versions are TB'ed, along with Janus B1 (we assume).
Now, if you go back to the future (Marty!), you will meet Melchior A2 (A2 meaning after the New Ocean Palace incident - truthfully by this time, we're probably on Melchior A2396) in 1000 AD and Belthasar A2 has since "died" and programmed a Nu to help you in 2300 AD. I don't think Gaspar ever gets to an A2 version, since we're not sure in what dimension / time line the End of Time operates. If it is only on Time Error, than nothing Crono and Co. do to the current timeline effects it, so Gaspar is still Gaspar A1.
The Magus that joing Crono and Co. is Janus A1. We see Janus B1 at the same time that we see Melchior B1. Janus A2 appears in 600 AD with the Black Omen overhead and is TB'ed at the time when Crono and Co. originally defeated Magus at his lair, and they were all thrown into a gate.