I don't know about that, but the game does seem to suggest that the
Raticate died. I mean, think about it. After he uses Raticate against you for the final time, your next battle is in Pokemon Tower, a Pokemon cemetery. Plus, he says he just caught a
Cubone, but he doesn't use one... ever. And he only has five Pokemon on hand during the battle, so it's not like he could have sent it to the PC. Plus, he gives you the Cubone excuse even if you fight him before getting the Silph Scope, in which case any Cubone in the tower would be unidentifiable and uncatchable.
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