Kate McCann was interviewed as a witness by the PJ on 4th May and 6th September 2007. She was also interviewed off the record, she says, by Neves and Encarnacao on 8th August, where they tried to get her to confess to something. Imo she was left in no doubt that their questions were not aimed at finding Madeleine.
Kate was under no illusion - as you rightly point out - that the Portuguese police and their case coordinator Amaral were no longer asking questions aimed to finding Madeleine or at the least what had happened to her.
That had not been their objective for quite some time - if it ever was.
Amaral's theory pointed the finger of accusation at Madeleine's parents. Prosecuting them was the be all and end all of "proving" Amaral's theory.
A tried and tested investigative technique is following the evidence which indicates the path leading to a conclusion.
It doesn't work if investigators invent a theory then try to fit evidence to suit particularly if there was no evidence or radically misinterpreted evidence to be had in the first instance.
Amaral doesn't know that. But everyone else does.