If your'e talking about the normal black bake on Teflon stuff in a smaller yellow aerosol can that Brownell's sells, no, it shouldn't mess up your heat treat. By directions, can only cure the stuff in the 300-350F range, which isn't hot enough to mess up any but the very lowest tempers. Least in any alloys I've looked at/heat treated. If you cook it hotter than this, supposedly burns it someway(believe was told the finish flakes off), so you may need to temper first, then use the Teflon.
This is jsut coming from memory, i can check my can at home if you need me too. If this is somethign you endup using often though, it is cheaper, and gives a better quality finish, to buy the stuff straight from the manufacturer in non aerosol format, and apply it with a spray gun. Or so I've been told by a friend who uses it often to refinish guns that come through his shop.
I haven't tried it on a knife yet, but I like results I got on magazine for my SKS. Plan on trying it on some knives sometime, just haven't finished any lately.