This is from an interview with Amaral at the time of the book launch. Perhaps he isn't so explicit in his book (I will have to force myself to re-read it at some point) but clearly this was his theory at the time:
Correio da Manhã - What do you think happened to the body?
Gonçalo Amaral – Everything indicated that the body, after having been at a certain location, was moved into another location by car, twenty something days later. With the residues that were found inside the car, the little girl had to have been transported inside it.
How can you state that?
Due to the type of fluid, we policemen, experts, say that the cadaver was frozen or preserved in the cold and when placed into the car boot, with the heat at that time [of the year], part of the ice melted. On a curb, for example, something fell from the trunk’s right side, above the wheel. It may be said that this is speculation, but it’s the only way to explain what happened there.