Nós simplesmente não sabemos. O tronco ou o dinheiro não aparecem em nenhuma das cenas posteriores (cronologicamente). Eles só desempenham um papel indireto como motivação de Teddy para obter o carro de Leonard. Existem apenas teorias sobre o paradeiro do dinheiro.
De imdb :
What happened to the money in the trunk of the Jaguar?
This question is never explicitly answered in the film, nor is there really any suggestion as to where it got to. It would appear that Nolan did not consider this a very important detail in his overall narrative of the film, but we may speculate. There are several possibilities that come to mind. (1) At the end of the story it could very well still be in the trunk ready for Leonard to rediscover it and wonder where it came from. (2) Leonard could have during the course of the film already added it to whatever stash of money he has been using for expenses. (3) Teddy could have broken into the car and taken it at some time during the film. (4) It is even possible that Natalie could have used a spare key (it is not unlikely that a couple living together would each have a key to the vehicles), found the money and taken it.