J.P. Morgan Chase & Co. has reached a settlement that will return an estimated $546 million to MF Global Holdings Ltd. customers, likely bringing an end to a major chapter in customers’ effort to recover money from the securities firm’s 2011 collapse. J.P. Morgan, the trustee for the failed company’s brokerage unit, and lawyers representing customer plaintiffs in the case filed their settlement agreement after finalizing terms in recent days, according to a person familiar with the process. Under terms of the settlement, filed in court Tuesday, J.P. Morgan is set to pay $100 million to reimburse customers, while also…