A Middlesex superior court judge denied Nathan Carman's motion to seal a nearly 3-year-old warrant.
The 23-year-old Middletown native survived a week at sea last fall but his mother disappeared during a fishing trip in September.
Linda Carman is presumed dead after their boat sank near Point Judith, Rhode Island.
Middlesex state's attorney Peter McShane argued the warrant, connected to the murder of Carman's grandfather, served on Nathan Carman's old apartment has been a public document since July 2014.
But Carman's attorney Trent LaLima argued it would damage his future at such a young age. In court on Thursday afternoon, the judge sided with the state.
Carman stayed silent as NBC Connecticut Troubleshooter Jill Konopka asked him questions outside of court on Thursday.
The 2014 warrant mentions there was an arrest warrant for Carman, in the murder of his grandfather John Chakalos, but it was never approved by a judge.
Chakalos was shot to death at his Windsor home back in December of 2013.
LaLima told the court of Carman's plans to become a successful businessman and community leader down the road; he called the documents damaging to Nathan's future.
Reiterating also, it is rare for this type of document to be made public before probable cause was established.
"The fact no arrests have been made in this, I do believe it is not a strong case against Mr. Carman. These are unsubstantiated allegations," LaLima said.
But McShane argued the document have been available to the press and public since July 2014.
"It just seems ironic for someone who wants to seal this, has appeared in 20/20 and numerous other outlets. Not exactly a low profile maintained by Mr. Carman," McShane added.
Carman has said he had no involvement in his grandfather's death.
Neither attorney would comment on camera after court. There was no update from the FBI or Windsor Police, and the cold case unit of the state's attorney's office said they continue to investigate.