Yes, the heat to powdercoat will damage the window.
My preferred method to remove the window is to carefully pry around the edge of the rubber seal with a not quite sharp knife edge. It needs to have enough of an edge to catch on the rim of the rubber seal, but not sharp enough to cut it. You just pry it out a little at a time, and slowly work your way all around. It may take a while, but this will get the window and seal out without damage so they can be reused. Last I knew, Richard had windows available if yours does need replaced.