You can very easily make a cut in the substrate with a circular saw and bury the cable in the cut.

Thanks for responding, Glenn.
We have a cement floor underneath the current carpet. Is that the same thing as the "substrate" ?
I just hope it's not too costly.

Cutting the concrete is messy and probably more expensive. But its an option. Have you looked into having it rerouted? Or is that not viable?

Most wiring for alarm contacts is just a pair of 22 gauge wires in a jacket, so it's very small. If this is what you have, I'd just rereoute (or replace) it along the edge of the floor and hide it in the gap between the flooring and the wall, underneath the base molding.

Thank you everyone.
We found a floor installer who says he can reroute the alarm wire around the perimeter of the room. It will be hidden under the 1/4 round/base shoe.
The other solution would be to install 2 wireless sensors at the 2 windows. This can also be done at a cost of about $200.
We're going to try to keep the same wire and re-routing it along the walls.
I hope it works.