How do you obtain another Master Ball after you have used the first one?
Solution 1:
To obtain another Master Ball after having already used the first one, you must have some luck on your side. The Goldenrod Radio Tower has a Lottery Corner, where if all 5 numbers of the ID of any of your Pokemon match (including those in the PC), you will receive a Master Ball. You can do this multiple times, but takes a lot of luck and patience.
You can also have a friend trade over a Pokemon with it holding a Master Ball.
If you have an Action Replay, you could use a code to get another Master Ball.