I once thought about this too, but time flows in certain ways in CT, notice every year that has had a connection to another year, progresses in time together, they've all gone ahead two years. they're allc onnected by time portals.
This is similiar reasoning as to why the group didn't lose their reason to search for marle after she blinkoed out of existance (if you think about it withouit marle in the future chrono would have never gotten the pendant to us ethe telepod to go back in time) but in Ct's world time and space operate differently, they 600Ad and 1000Ad were connected so the progress together and Chrono and Lucca were already back in time before Marle blinked out of existance.