The hex orientation will change. Bee comb normally is made with the hex vertex on the bottom, ⬢. If you turn the foundation you put the hex flat on the bottom, ⬣. I don't know if that will mess with the bees. The Lusby's claimed that bees used the Y and ⅄ vertices made by back to back hexagons for in hive navigation. I don't know the scientific basis for their claim or if there even is one, just that they made it and I remain a bit skeptical because bees seem to have no problems with plastic. If they weren't full of it then it would be inadvisable.
Why not just use a standard 8-1/2 inch deep foundation sheet and let them build the rest with natural comb, its only an extra 1-5/8 inches? It will help keep the girls from making drone comb in other places and you could easily cull excess drone comb that way.