Thursday’s ninth circuit appellate court ruling to uphold a nationwide restraining order on Donald Trump’s controversial travel ban was heralded as a major blow to the administration and a victory for migrant rights advocates and refugee resettlement agencies across the country.

In many respects the ruling has left the administration in a state of disarray. Though he had vowed to fight the ruling in court, on Friday, the president said he was considering signing a “brand new” executive order on immigration instead.

Migrants and refugees with valid documentation from the seven targeted Muslim-majority countries have been allowed to enter the United States as the Department of Homeland Security announced last week it would obey the federal court order.

But the restraining order itself only applies to certain sections of Trump’s sprawling executive action, and does not apply to the president’s directive to vastly curtail the number of refugees resettled in the US each year by more than half.

Trump’s executive order, announced two weeks ago, was in stark contrast to Barack Obama’s pledge last September to significantly increase the United States’ annual resettlement targets to 110,000 for the 2017 fiscal year, which began in October 2016. The state department responded to Obama’s order by accelerating the rate of heavily vetted refugee arrivals to meet this target. By the first quarter of 2017, the US had admitted 25,671 refugees, compared with 13,791 the year before.

This increased volume of resettlements is set to collide with elements of Trump’s controversial order that have remained intact, namely the decision to limit the annual intake of refugees to 50,000 a year. If the US continues to accept refugees at the rate it has done for the first quarter, it will reach the 50,000 cap by March – meaning the resettlement program will effectively be suspended anyway until October 2017.

David Miliband, the former UK foreign secretary and chief executive of the International Rescue Committee, one of the largest refugee resettlement agencies working in America, said on Thursday that the appellate court ruling would allow his organisation to “get back to work resettling refugees”. But seen in the context of Trump’s drastic cap the picture may be more complicated. The latest statistics show that by the end of January 2017 the US had already resettled more than 32,000 people.

Questions also remain over the tens of thousands of refugees currently referred by the UN’s refugee agency, UNHCR, for resettlement to the US. Last year the agency referred a record number of refugees to the federal government, indicative of the magnitude of the world’s refugee crisis, which has left more than 65 million people displaced across the world. The average vetting time for these referrals is 18 months to two years to complete – meaning the vast majority are still in the so-called resettlement pipeline. The UN has referred more than 60,000 Syrian refugees to the US for vetting alone. Last year the agency referred more than 7,000 Somalis and 7,000 Iraqis for vetting.

Even if Trump’s order is eventually deemed unconstitutional by the supreme court, it will still have the ability to turn down thousands of the world’s neediest people from the areas he targeted in the order last month.