Maharashtra ATS, which earlier probed the case, had alleged in its charge sheets that Thakur attended several conspiracy meetings held by the right wing group Abhinav Bharat in Bhopal, Indore, Faridabad, Dharamkot and Ujjain.
It claimed key witnesses had heard Thakur discussing the conspiracy at a closed-door meeting in Bhopal on April 11, 2008, it said.
ATS recovered the laptop, seized its hard disk for examination at FSL labs, and cited a host of audio and video clips retrieved from it to back its claims.
The division bench headed by Justice R V More, which was hearing Thakur's bail plea today, was informed about the meeting by advocate B A Desai, who appeared for blast victims.
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When the HC asked NIA to produce the transcript of the recording of the Bhopal meeting, the agency said it was not aware if it existed.
"The Faridabad meeting was held before the Bhopal meeting and the reference to the accused was first made in the Bhopal meeting. So, if you have transcripts of the first meeting, the transcripts of the subsequent meetings must be there. What did you do with them? These were crucial meetings and the transcripts are important evidence. So, how are they missing?" the bench asked.