When Donald Trump launched his war against Iran in late February, he had ambitious goals: to topple Iran’s theocratic regime, destroy its military capabilities and nuclear program, and instigate a popular uprising by Iranians. A week into the war, Trump said he would only accept Iran’s “unconditional surrender”. On Sunday, Trump settled for a deal that reopens the strait of Hormuz.

The US president celebrated having solved a problem he had created: reopening a vital waterway through which more than a fifth of the world’s oil supply passed each day – before Iran effectively closed it at the start of the war, increasing energy prices and disrupting the global economy. “Ships of the World, start your engines,” Trump wrote on social media in announcing the latest deal. “Let the oil flow!”

This isn’t a typical case of Trump making grandiose claims, declaring victory and moving on to his next obsession. Trump cornered himself by starting a war of choice, along with Israel, aimed at regime change in Tehran. But Iran withstood weeks of intense bombing by two of the world’s most powerful militaries, and its rulers emerged more defiant and with greater leverage than they had before the conflict. The regime turned its geographic proximity to the strait of Hormuz into a new weapon that allows it to disrupt shipments of not just oil and liquified natural gas, but fertilizer and other key agricultural products that could instigate global food shortages. Iran knows it can’t fight a head-on battle with the US military, but Trump showed its leaders that they could hold the world’s economy hostage.

And the much-hyped deal, which is expected to be formally signed on Friday in Geneva, doesn’t end the war. It’s essentially a 60-day extension of a ceasefire that was reached between Iran and the US on 8 April, but did not lead to the reopening of the strait of Hormuz because Trump then imposed a naval blockade against Iranian ships in the region. Several rounds of negotiations also stalled over multiple violations of the ceasefire, and as Trump wavered between making a deal and issuing threats to restart the war.

While the final text of the latest agreement has not yet been released, it once again deferred the most difficult questions to future negotiations. Those talks are supposed to conclude within 60 days of the deal’s signing on 19 June, but they’re likely to continue for months, if not years. In other words, Trump and Iran bought at least two months of breathing space for diplomacy to resolve what bombing could not. And while neither Trump nor Iran’s leaders have an interest in resuming an all-out war, there’s no guarantee that the two sides won’t fight another round.

The unresolved questions are daunting – and they’re the same ones that faced US and Iranian negotiators during their last round of talks in Geneva, held 48 hours before Trump launched the war on 28 February. Those negotiations, which were mediated by Oman, involved the Iranian foreign minister, Abbas Araghchi, and two of Trump’s most trusted advisers: his special envoy to the Middle East, Steve Witkoff, and his son-in-law, Jared Kushner. The UK’s national security adviser, Jonathan Powell, also attended the talks, although it’s unclear if he participated directly. Sources told the Guardian that Powell found Iran’s offer to curtail its nuclear program “surprising” – and significant enough to continue negotiations and avoid a rush to war.

Iran is unlikely to offer the same concessions on its nuclear enrichment that it did in the last round of talks. The Iranian regime is emboldened, having survived the assassination of its top leaders and weeks of severe bombardment. In the war’s early hours, joint US-Israeli airstrikes killed more than 30 top Iranian military and political officials, including the supreme leader, Ayatollah Ali Khamenei.

That early success seduced Trump into thinking he could achieve a quick military victory and topple the Islamic regime that rose to power after Iran’s 1979 revolution. But Iranian leaders rallied around the regime and quickly installed Khamenei’s son, Mojtaba, as the new supreme leader. The younger Khamenei is backed by hardline officers of the Islamic Revolutionary Guard Corps (IRGC), Iran’s most powerful military force, which now exerts even greater influence over the country’s economy and political system.

In upcoming negotiations, the Revolutionary Guards and other regime factions are likely to push for Iran’s longterm control over the strait of Hormuz, including continuing to impose fees for “maritime services” on commercial ships passing through the waterway. Trump insists that the strait will remain “permanently toll-free,” but the agreement announced on Sunday only suspended tolls (which Iran had started charging during the war) for 60 days. Any lasting arrangements will be negotiated between the US, Iran and other countries in the region, including Oman, which also borders the strait of Hormuz.

Already, Iranian officials are floating rationales to collect not an outright toll for passing vessels, but what they call fees for “navigation and security” services – even though these levies did not exist before the war. “Only Iran and Oman have the right to receive these fees and no other party can decide about it,” said Mehdi Mohammadi, an adviser to Iran’s chief negotiator and speaker of parliament, Mohammad-Bagher Ghalibaf. “This process is in place now and will remain in place in any future agreement.”

It would be embarrassing for Trump and his administration to allow Iran to impose tolls (even if they’re shared with its neighbor, Oman) on a waterway that has historically had freedom of navigation. But the president and his aides must also realize that they might not be able to negotiate their way back to the prewar status quo. Trump’s ill-fated war emboldened Iran – and its leaders will seek to extract a higher price for future concessions.

Aside from the future status of the strait of Hormuz, and limitations on Iran’s nuclear program and future capabilities, other difficult questions have been deferred to later negotiations. These include the fate of Iran’s stockpile of more than 400kg of uranium, which has been enriched up to 60% purity – not far from the 90% level required to build a nuclear device. Iran will likely seek significant relief from US and other international economic sanctions in exchange for diluting its existing uranium stockpile and agreeing to limits on future enrichment, which would allow it to operate power plants but not to produce nuclear weapons.

Benjamin Netanyahu, the Israeli prime minister who spent months convincing Trump to launch his regime-change war, has insisted that any deal should also limit Tehran’s ability to develop ballistic missiles as well as its support for regional militias, including Hamas in Gaza, Hezbollah in Lebanon and the Houthis in Yemen. On 28 February, Trump had listed those same concerns among the reasons he decided to take the US to war, arguing that Iran posed an imminent threat to Americans.

All of these questions are still unresolved, and some of them could torpedo the latest agreement and upcoming negotiations. For now, Trump has agreed to at least 60 days of peace – and he seems more eager to make a grand deal with an Iranian regime he could not overthrow.

• Mohamad Bazzi is a Guardian US columnist. He is also director of the Center for Near Eastern Studies, and a journalism professor, at New York University