I would imagine that the existing track wont be abandoned. This will just be a spur.GTAA’s master plan looks like this (on page 83)
View attachment 241697
Basically just a super long tunnel. the legend is on the right if you can read it, orange is tunnel and red is at grade.
Also seems like the Woodbine GO station is not taken into account (was this made before Woodbine GO was a thing?)