First of all, I would like to make you aware that this downhill trek is a dangerous one, more so because it's monsoon time right now.
I travelled on this in April, that too when there was a 2 hour block on the DN line.
I would suggest you to take the UP line (the leftmost one) when starting downhill from Khandala. Because the tunnel on DN line is 2.3 kms long, and it will be dangerous to walk so long inside it. UP line also has tunnel, but it is smaller and...
more... the tunnel is also new, so more clearance. Still be careful.
Once the long tunnel is gone, when the 3 tracks meet again beneath the Mumbai Pune expressway, you can take the DN line (right most) from then on.
Cheers. Be safe n enjoy. :-)