Why did the police and prosecution continue to press the charges against Amanda and Raffaele after the authorities absolutely knew that Rudy Guede had been the one who murdered and raped Meredith?
The police had arrested Patrick Lumumba and had mistreated him rather severely to force him to make a false statement, but apparently he did not buckle. The police and judiciary released Lumumba after the Swiss professor gave him a strong alibi and Guede's role became strongly evident. However, the police maintained some control over Lumumba, keeping his bar closed as a crime scene and continuing to monitor (tap) his phone. Lumumba initially complained of police mistreatment, but then abandoned his award for false arrest (IIUC) and joined the prosecution of Amanda and Raffaele as a civil party; his lawyer made prejudicial comments against Amanda in court. Eventually Lumumba left Italy for Poland, his wife's native country (IIUC) without applying to the ECHR about his unfair treatment.
The police mistreated Amanda and Raffaele and were able to obtain false statements from both of them on Nov. 5/6. Amanda also wrote a Memoriale 1 in which she described some of the mistreatment she received during the interrogation by the police. I suspect that this disclosure by her, which she repeated, and which her parents publicly stated, made the police, prosecution, and the more corrupt of the judges realize that for the self-protection of the corrupt police, prosecutor, and investigating judge they must railroad Amanda and Raffaele, find them guilty of murder and rape, and keep them in prison (at least until the statute of limitations on the crimes of the authorities ran out).
What the police, prosecution, and corrupt judges were avoiding by their continued wrongful prosecution of Amanda and Raffaele was any investigation and prosecution of the corrupt behavior of the authorities. Under CP 377-bis, the police and prosecutor and any other authorities who had threatened or used violence to get Amanda or Raffaele to sign false statements for presentation to the judicial authority could, if convicted, been sentenced to from 2 to 6 years in prison.
The text of CP 377-bis is provided in Italian and Google-Translate English in post #2574.
This post includes a copy of part of my post on IIP/IAF.
ETA: Hellmann, after his retirement, expressed some misgiving for convicting Amanda of calunnia, but stated (IIRC) he had to do that or say that the police had committed a crime. The crime the police had committed is the one described in CP 377-bis. The Chieffi annulment of Hellmann and the Nencini provisional conviction are ways the judiciary are backing up the police from any accountability with respect to this Italian law.