Lynn, 60, denies murdering Carol Clay, 73, who went missing from Victoria's High Country while camping in March 2020 with her friend Russell Hill, 74.
The former Jetstar pilot was granted a retrial in December after an appeal court found he had suffered a substantial miscarriage of justice in his first trial.
He made a bid for freedom in the Victorian Supreme Court, where he testified about his "disgusting" conditions in custody.
Lynn said he had been assaulted with faeces and placed in the "dungeon", or solitary confinement, because it was not safe for him to be around other inmates, who had identified him as "Greg Lynn from TV".
He also claimed he was assaulted a second time in July, when an inmate poked and spat on him after Lynn accused the man of being a police informer.
"He confronted me and was just ready to explode, like Vesuvius ready to erupt," Lynn said in evidence during his bail application.
"He mentioned he had killed before and he would kill again ... and then he made an insult that I was a killer of old people.
"My response was that I hadn't killed anyone."
Prosecutors opposed bail but Lynn's barrister Dermot Dann KC argued his client's vulnerability in custody and the long time he had spent on remand were exceptional reasons for him to be released.
Chief Justice Richard Niall disagreed, finding Lynn's circumstances were not exceptional as he refused bail on Tuesday morning.
The chief judge accepted there would be a significant period of time between Lynn's successful appeal and his retrial, which is due to start in May.
But a delay of 12 to 18 months was not outside the usual range for a murder case, Justice Niall said.
He also did not regard Lynn's conditions in custody as exceptional, although he did accept the accused killer's time behind bars had been difficult.
The judge remanded Lynn in custody ahead of his retrial in May.
Lynn's son Geordie was in court for the decision but did not respond to questions from reporters as he left.
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