Are you talking about your home command station? That command station can't ever be replaced, and you'll actually notice its stats are better than a MK3 economic station by a fair bit, so you wouldn't even want to.
The only station you can't replace is the one on your home system, as that one is kind of like your king in Chess. But for any other systems, just placing the new station will delete the old one. You can't place it exactly on top of your existing station, but you can put it somewhere it fits and then it will all just automatically shift.