No, it doesn't wipe out the old key.
What you may want to do is, buy two keys from the locksmith, let them cut both of them for you, but DO NOT let them program the third key. Program that one yourself by doing the hokey pokey with the lock and doors. There's instructions on here on the process.
For the hokey pokey to work, you have to have two different keys. Your original, and the one the locksmith programmed with their computer.
Now, do the hokey pokey with the locksmith key and your key. Then program the third yourself, right there in the parking lot of the locksmith. If the key won't program, and you get a red flashing light on your dash instead of the key actually working, they did something wrong, and you'll never get the remote start to work. Have them fix the glitch.