I'm not sure if this has already been said, but if you talk to the Lucca "ghost" before going to the DBT to kill the time Devourer, Lucca very clearly says: "I'm sorry, Kid, we no longer exist in this timeline."
Meaning, that Marle, Lucca, and Crono all bit the dust in the Home timeline. I'm trying to remember when the timelines split... 1010, right? Since the fall of Guardia was in 1005, and if Crono and Marle died then, then they're gone for good, no matter how the timelines merge.
Of course, I have an idea about Porre. Lynx was an agent of Porre, supposedly, right? Is it possible that Porre's assistance "from beyond the normal flow of time" was part of Project Kid? It gave Lynx a reason to be in El Nido and talk with Viper..
But I still can't remember if he was part of the Porre thing. Porre's invasion of El Nido might've been necessary for Serge to finally end up at Opassa Beach (to get the TD)... so, is it possible that in a new timeline, Porre would not be a military power and Guardia would not fall?