The federal judge overseeing Donald Trump’s prosecution on charges of retaining classified documents denied his effort to have the case dismissed on the contention that the Presidential Records Act allowed him to transform them as personal property and possess them at his Mar-a-Lago club.

The ruling by US district judge Aileen Cannon was significant as it struck one of Trump’s main defenses and suggested the case is headed to trial.

Related: Trump appeals ruling letting Fani Willis stay on election interference case

Cannon’s three-page order rejecting Trump’s motion to dismiss rested on the fact that Trump’s argument about the Presidential Records Act did not directly address the applicability of the Espionage Act, which he has been charged with violating, meaning it did not give her a basis to toss the case.

But the order left open the possibility that Trump could raise his Presidential Records Act theory as a defense at trial, and the possibility that Cannon could instruct the jury to credit Trump’s theory in such a beneficial manner that it could potentially ensure Trump’s acquittal.

The way the jury might be directed has become a major source of anxiety for prosecutors in the office of special counsel Jack Smith, after the judge last month ordered both sides to draft jury instructions envisioning two possible scenarios that gave extraordinary credit to Trump’s defenses.

Cannon had asked Trump and prosecutors to each draft jury instructions supposing it was true that Trump had the power under the Presidential Records Act to turn any White House document into personal records – which would implicitly mean he was authorized to retain them.

The authorization issue is key to the case because Trump was indicted for unlawfully retaining national security materials under the Espionage Act. If Trump could show that he was somehow authorized to keep the documents at Mar-a-Lago, it would preclude his prosecution.

Even more crucial is if Cannon actually uses such instructions at trial, because if that happens after the jury is sworn in, double jeopardy protections for Trump would kick in. If Trump is then acquitted, prosecutors would not be allowed to retry the case.

The first scenario envisioned that it was up to the jury to decide whether prosecutors could show beyond a reasonable doubt that Trump had not designated each classified document he took to Mar-a-Lago as personal.

The second scenario envisioned that Trump had the “sole authority” to turn a document he came across as president into a personal record that he could keep, and the very fact that he took them with him to Mar-a-Lago meant it was a personal record.

Prosecutors responded to Cannon with a sharply-worded 24-page filing on Tuesday that made clear they thought both scenarios were wrong on the law, but indicated they could find a way to work with the first scenario, because proving the classified documents were not personal was feasible.

But prosecutors wrote the second scenario was fatal to their case because it allowed Trump to simply claim all the classified documents seized at Mar-a-Lago were his personal property by virtue of taking them with him – and prosecutors would have no way to dispute that claim.

Related: Exclusive: Trump Media saved in 2022 by Russian-American under criminal investigation

The Tuesday filing marked a moment of frustration for prosecutors, and they demanded that Cannon promptly articulate whether she intended to endorse a “fundamentally flawed legal premise” so they could appeal or have a higher court directly instruct how she should proceed with a writ of mandamus.

That demand earned prosecutors a stinging rebuke from Cannon, who called their request “unprecedented” and “unjust”.

Cannon wrote the she was declining to make known her position on how she would instruct the jury and told prosecutors her solicitation of draft jury instructions was an attempt to better understand both sides’ positions in a case where the issues at hand had never previously been litigated.

Trump faces 40 charges arising from his retention of classified information after leaving the White House and alleged obstruction of attempts to recover such records. He has pleaded not guilty.

Separately, earlier it emerged Trump is scheduled to be deposed in a civil case in New York, by lawyers for co-founders of his social media company as part of a dispute over ownership in Trump Media & Technology Group.

A notice filed with Delaware’s court of chancery, where the co-founders sued Trump Media, said the deposition is scheduled for 15 April at 10am ET in New York.

Also on 15 April, jury selection will begin in a court in Manhattan in the first ever criminal trial of a former US president, related to payments to Stormy Daniels and a subsequent financial cover-up during the 2016 election. Trump denies the charges.

In the civil case, the notice of deposition did not specify the questions. The parties involved did not comment. Trump Media, the controversial company which owns the Truth Social messaging platform, began trading on the stock market last week.

Depositions often get rescheduled.

The company was sued in February by Andy Litinsky and Wes Moss, two former contestants on Trump’s reality TV show The Apprentice.

They accused Trump Media of denying them their stake, which they own through their United Atlantic Ventures partnership, by trying to dilute their stock and by preventing them from selling it.

Trump then also sued Litinsky and Moss, in Florida on 24 March, and is seeking to strip them of their stock, saying they failed to earn it, because of mismanagement. The parties did not respond to requests for comment on Thursday.

Meanwhile, a Georgia judge on Thursday rejected Trump’s bid to dismiss criminal charges in the state’s 2020 election interference case against him, which the former US president argued violate his free speech rights.

Related: Only in Atlanta: the small-town scandal of the Trump-Fani Willis case

The Fulton county superior court judge Scott McAfee found that the indictment alleges statements by Trump and others charged in the case were made “in furtherance of criminal activity” and are not protected by the first amendment to the US constitution, that protects free speech.

Trump and the other defendants have been charged with racketeering and other offenses over their effort to overturn Trump’s defeat in Georgia in the 2020 presidential election to Joe Biden, who was inaugurated in 2021 despite a long campaign by Trump in multiple fora to reverse the result.

Biden is now running for re-election, as the presumptive Democratic party nominee, while Trump is the presumptive Republican nominee following a primary season where he saw off multiple challengers despite being a defendant in several criminal and civil court cases. The defendants in the Georgia case have pleaded not guilty.

The Georgia charges focus on attempts to assemble an alternate slate of presidential electors pledged to vote for Trump – despite Biden’s historic win in the state – and Trump’s January 2021 phone call urging the state’s top election official to “find” enough votes to overturn his narrow defeat.

McAfee’s ruling is a signal he will continue moving the case toward trial even as Trump and eight co-defendants continue their efforts to disqualify the district attorney, Fani Willis, the prosecutor overseeing the case. A Georgia appeals court is set to decide whether to take up that issue in the coming weeks.

McAfee said it will be up to a jury to determine if Trump and other defendants, which include his former personal lawyer, Rudy Giuliani, and former chief of staff, Mark Meadows, acted with criminal intent.

Trump has other pending challenges to the case, including a claim that he is immune from charges tied to official actions he took as president.

Reuters contributed reporting