Even for August, the federal court complex in Newark has been eerily quiet over the past week. Trials adjourned. Guilty pleas put on hold. Hearings canceled, to be rescheduled once the confusion passes.

The court has all but reached a standstill — and may stay there for months — after a judge raised questions about the legitimacy of New Jersey’s top federal prosecutor, Alina Habba.

Ms. Habba, a former personal lawyer to President Trump, has led the U.S. attorney’s office since late March, courting controversy as she pursued high-profile cases against local Democrats.

Last month, the Justice Department resorted to an extraordinary series of legal maneuvers to keep her in office. Last week, a judge ruled that those moves had been unconstitutional and said that Ms. Habba had not been the lawful leader of the office since July 1.

Had the judge’s order taken effect immediately, Ms. Habba would have been disqualified from participating in ongoing cases. But the judge, Matthew W. Brann of the Middle District of Pennsylvania, placed on hold any effect of his ruling pertaining to Ms. Habba, so that an appeals court could consider the case.

Nonetheless, the courts are bracing for the possibility that any proceedings Ms. Habba has touched, or those involving prosecutors she supervises, could be challenged by defense lawyers.