(CNN) From inside a Texas prison cell, polygamous prophet Warren Jeffs is orchestrating a shakeup of his embattled sect, the Fundamentalist Church of Jesus Christ of Latter Day Saints, federal prosecutors allege in court documents filed Monday.

Jeffs, who is serving a life prison sentence for sexually assaulting his underage brides at an FLDS compound in Texas, has gone so far as to order a complete reorganization of the FLDS leadership, prosecutors allege. The disclosures came in a court filing seeking to keep other sect leaders behind bars as they await trial in a welfare fraud case

A hearing on the matter is set Tuesday in federal court in Salt Lake City.

The court documents reveal the inner turmoil of a sect under pressure from federal authorities as well as "apostates," former members who remain in the vicinity of the FLDS home base of Short Creek, the abutting communities of Hildale, Utah, and Colorado City, Arizona.

They also show that the FBI is closely watching the FLDS. Some of the reports attached to the government's motion were compiled as recently as Friday.

Earlier this year, a federal jury in Phoenix found the FLDS discriminated against non-members in Short Creek . Four days have been set aside in October for testimony concerning what should be done with the governments of the two cities and their shared police department.

As testimony in the Phoenix case wound down, federal prosecutors in Salt Lake City announced the indictment of 11 FLDS members, including Lyle Jeffs . They are accused of comingling food stamp benefits and distributing purchased items in accordance with a member's rank in the sect. Church leaders and United Order members received the best of everything, while less favored members barely scraped by, federal authorities allege.

Lyle Jeffs is a federal fugitive from those charges, having fled home detention in Salt Lake City. FBI officials suggested he used olive oil to slip out of his ankle monitor.

Included among the documents are FBI reports, letters from Jeffs, news and weather clippings concerning natural disasters, wars and other mass tragedies, what appears to be a list of every FLDS follower living in Short Creek.

The documents indicate that Warren Jeffs has named a new bishop of Short Creek, replacing one brother, Lyle, with another, Nephi. The prophet also has abolished his sect's elite United Order, which was established under Lyle. The prophet has placed his followers on "restoral status," meaning they must renew their commitment to the FLDS. "My church order are out of order," Jeffs wrote in his distinctive block printing in a June 3 letter to his flock. He added that the "bishop's assistant," Ben Johnson , "is of no priesthood and needs go far away on repenting labor" and is barred from communicating with other members.

One FBI report documenting a prison visit by two Jeffs wives, suggests that even the newly installed bishop faces stern words and detailed instructions from the prophet. Warren Jeffs noted in his lengthy instructions to Nephi that each of Short Creek's recent bishops had failed: "Each one has had the great sin of finding comfort in women's attention," Warren Jeffs said, warning: "Do not gossip with the family of Warren Jeffs."

He explained that he had removed Lyle Jeffs as bishop after "a short revelation" and that all members would be re-interviewed, re-baptized and re-confirmed into the United Order. He asked for and received the names of every United Order member who was in good standing during Lyle Jeffs' tenure as bishop.

And, Warren Jeffs wrote in a lengthy letter dated June 3, anyone who doesn't pass muster will be banished and sent "far away."

The documents also reveal how another Jeffs brother, Seth, and another leader, John Wayman, allegedly violated terms of their release on bond: They were supposed to avoid contact but met secretly after midnight on several evenings at the FLDS meeting house in Short Creek to discuss how to carry out the prophet's orders.