Of course you can.

IMO, the piece of Flexwatt in your rack is not long enough to experience that much drop just do to length alone. More than likely, a part of your heater is contacting more surface that is conducting the heat away, or you have a damaged area that increased resistance.

Back to cutting flexwatt -
A good way is to use a single piece for every two shelves, just to save on connectors and such.