What your described is exactly how it is designed to work. You cannot "add on a key" you reprogram all keys at once. Any time you need to replace a key you need every key at the same time and the car forgets any old keys and learns them all fresh.

Re do what you did with all keys and you'll have them all working.

If the remote dies on an original key you can swap the guts from the spare eBay key if the 8pin chip with the imobilizer is moved over and get a replacement key that remotes and starts the car. You can even get a blank cut if needed.