It will be more difficult to pop the knot into the sandwich but I think I would still try. Instead of just pulling and taking the chance of breaking the thread in the fabric, I would pull the knot to where I wanted to pop it through and then back it off a little. I would then take a pin and carefully push the threads of the fabric aside enough to pop the knot through. Once the knot is buried I would coax the threads of the fabric back to close the hole.