After further inspection, they actually cut the old windows out and left the old border of the windows stitched in. Then just sowed the new windows on top of the old. I'm calling them tomorrow about it.
I've seen new eisenglass stitched over the old the way the OP described. It's a cheap way to get windows you can see through. Removing the old stuff completely and stitching in new costs more. Replacing the enclosure entirely (glass and canvas) costs the most.
