I would love to see a cost breakdown of how much money really was saved by using the old CN rail tunnel vs just boring a new tunnel next to it, considering all of these complications. Of course you would have to factor in any refurbishment to the old tunnel that would need to be done that now would not be needed due to this rebuild.
However, if the cost was close, then this is an epic fail. It would have been much more wise in that case to build a new tunnel for the REM, as this effectively killed the ability to have VIA and other trains continue into Garre Central from the East. Two tunnels are always better than one.
What's really scary is that all these issues showcase how unsafe the tunnel really was during commuter rail times.