No investigation was ever carried out to find out who allegedly tortured her and she was convicted of perjury. Some believe that she was beaten up in prison by fellow prisoners.
I believe that as a result of having a bag over her head she could not see the officers who were beating her and therefore could not identify them, she did attest to Amaral's presence so he did know what was going on whether or not he took part physically. His presence condoned.
The court however decided she had been tortured ... hence Amaral's conviction for perjury.
Why the outcome for her was an addition to her sentence is perhaps just another vagary of Portuguese justice.
Some have lied that she was beaten elsewhere ... fortunately the prison governor dealt with that particular calumny in an effective manner which totally refuted the allegation.
Neither in Joana's case nor in Madeleine's case could it be said either was his finest hour.