Bayer has agreed to thousands of legal settlements over Monsanto’s weed killer Roundup after a federal judge raised questions about a deal pegged at up to $10.9 billion that had failed to resolve all the litigation, according to a court filing Thursday.

In a case management statement, filed in the multidistrict litigation in the Northern District of California, lawyers wrote that “master settlement agreements have now been reached” with three leading plaintiffs firms, resolving about 12,000 Roundup cases in state and federal courts. The filing comes after U.S. District Judge Vince Chhabria of the Northern District of California, who oversees the multidistrict litigation, called a hearing last month to discuss the settlement after receiving numerous confidential letters from plaintiffs attorneys insisting that Bayer had reneged on their agreements.