While I can think of no security theater reason why not to allow it, my inbound YYZ flights all have ITD stamped on the BP. That means nothing to mortals, so it must mean something to them.

But you should be able to get the two flights linked in EWR and the second BP printed as such.

Others are saying all is OK, but I'm not a huge fan of being in the wrong part of places where the theater is out in force.