Pokemon trading between two gen II games on the GBA SP

So, here's what I've managed to find out on my own:

1- With the Transfer Pak connected, there is another section added to the Pokemon Selection screen when you are preparing a Free Battle, which allows you to enter and register a team from your Gameboy Color game (it grants instant access to every legal option in your party and all of your boxes).

2- As mentioned above, you can register a team from your Gameboy Color game. This allows you to plug in your game, register your team, turn the N64 off, plug in your friend's game, register their team, and so on, allowing multiple people to play with their Gameboy Color teams without requiring multiple Transfer Paks at once. However, from what I can tell, you can only register teams for games using Preset Rules; if you're using a Custom Ruleset, you cannot register a team.

Unfortunately, when your nephew created a new save file a significant portion of the data will have been overwritten, so complete recovery is impossible and even partial recovery is completely unfeasible. The cartridge only has a limited amount of memory to write on. In order to make room for your nephews save, it had to make new space by writing over place where your data was. Since the kind of sophisticated programs used for hard drive recovery are not available for gba cartridges, you are out of luck.

The difference between recovering data from a computer and a cartridge is a combination of the lack of programs and access to the cartridge, and the fact that the creation of a new file overwrites a significant amount of data. Its not like a computer where the data is still there but not easy for the computer to find