The violence had left 41 people dead and scores injured.
Honeypreet, who claims to be an adopted daughter of the Dera chief, and eleven others have been charged with sedition, criminal conspiracy, besides other offences under the Indian Penal Code (IPC).
Three others have been charged under Section 216 of the IPC (Harbouring offender who has escaped from custody or whose apprehension has been ordered) for giving shelter to Honeypreet when she was on the run, Panchkula Police Commissioner A S Chawla said.
A lookout notice, and later an arrest warrant, was issued by the Haryana Police against Honeypreet before she was arrested last month.
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The Dera chief has been sentenced to 20 years in prison for allegedly raping two female disciples.
Honeypreet and the eleven others, including Dilawar Insan, Surinder Dhiman, and Chamkaur Singh, have been charged under Sections including 121 (waging, or attempting to wage war, or abetting waging of war, against the government) and 121-A (conspiracy to commit offences) of IPC.
Honeypreet, whose real name is Priyanka Taneja, currently in judicial remand in the Ambala central jail since October 14, was arrested by the Haryana police on October 4.
Cash recovery from Chamkaur Singh and documents seized from Honeypreet are among evidences that form part of the 979-page charge sheet, according to officials.
During Honeypreet's remand, the police had recovered a mobile phone, a laptop, some credit and debit cards and documents of properties and education-related certificates belonging to her.
According to the police, as many as 173 FIRs with nearly 1,000 Dera followers as accused for attacking security forces and damaging public property have been registered so far.
Panchkula police commissioner Chawla said the SIT had completed the formalities before presenting of the charge sheet.
According to the rules, the investigating team has to take an approval from the government before charge-sheeting the accused in a sedition case for waging war against the state.