Cool pool,
It would work just as long as you don't get too close or too hot. Trust me, I know from experience that you can melt a hole in the covering if you get too close with the heat gun. The only you have is going to put out a lot of heat so be careful. If you say you can adjust the temp on it I would set it to the lowest temp and then adjust from there. Move it up if you can see the covering being affected by the heat. Monokote temperature is 250 degrees, so you want that to be your target temperature. Just start low and work up.

Hope this helps

Ken