The facts are in the files and they are facts, Gonçalo Amaral did not invent "facts". What the judge said was that it was not within her remit to investigate the disappearance.
I'd agree that she said that investigating the truthfulness of the "facts" was not the subject-matter of the trial.
Was CdaM justified in asserting that RM had had sex with a cat and tortured various other animals as well? There was a statement to that effect in the files, but it doesn't mean that it was true.
I could have stated (hypothetically) that you were a spy for an enemy power intent on clearing the Algarve of the tourist industry to make way for a North Korean intercontinental missile launchpad... if I had made a statement to that effect, it wouldn't make it "true", either, would it?
She stated that for "the main part" the facts that were the basis could be found in the files. Not that ALL were.
There are several "facts" that simply are not in the accessible files. The only thing that would be "true" is that I'd made a statement to that effect.
And, if an author had decided to only discuss the possibility of a (hypothetical) North Korean missile launchpad, even when that possibility later appeared to be highly unlikely, what then? Is that version the "truth"?