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Jones attempted to fight in court to have the quarantine lifted and prevent officials from having the animals culled, but the agency announced plans April 2 to have the 31 remaining sheep in the flock destroyed.
However, the sheep disappeared from the ranch earlier this month, with a group calling itself the Farmers' Peace Corps taking responsibility in a note.
"We have taken the animals into protective custody until an alternative to killing has been found, or conclusive independent proof or clear evidence of disease has been proven. This has been done without the knowledge or participation of the owner," the note read.
Police said they are searching for the thieves and the flock.