Caravan was able to come to conclusion the hard disk had malware becuase part of legal proceedings evidence is provided to all parties of the case. In this case the pune police gave a true copy for on the activists rona wilson. But has not yet shared copies of others hard disks.
All electornic evidence is collected and submitted to the court under Section 65B of the Evidence Act. This provision of the Evidence Act allows submission of evidence. https://indiankanoon.org/doc/35556724/ 
The collection of evidence under section 65B requires the police or any other authority to provide the receipts of evidence under the section and has to ensure the electronic information is not tampered with. But most of the time the police aren't trained for this.
In case this is not done by the book, it is easy to tamper with electronic evidence. Which is why it is important the due process and a copy of evidence is given to you at collection stage, not part of court submission. section 65 B(4) describes what needs to be done.
What is happening in bhima koregaon is a clear case of political vendetta of the state against human rights activists. But the state is now employing methods of electronic surveillance and manipulation to build flase cases.
This manipulation of evidence is not new, but by employing secretive unwaranted cyber weapons, the state is threatening everyone who might want to question its practices. These systemic changes can't be fought by individuals but needs a relook at state power.
Reforms of the evidence act won't fix these problems. We need to re-look at state surveillance practices and need to force them to be accountable there. While we have a right to privacy, the state is ignoring to translate these rights by not making the laws.
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