It sounds like the money was already transferred back to the EPA and Citi doesn't even have it anymore.
Citi has money, and money is fungible. The Judge is basically taking the stance that if Trump won't pay the NGOs, and she can't force Trump to do it, Citi can just pay them instead and then Citi can hope Trump reimburses them / Citi can steal it from other Government funds / Citi can sue the Trump Admin.
Citi's insane if they pay this out, but at the same time, Citi doesn't have the same inherent protections that Trump and the Trump admin has. The Judge actually could, perhaps, go after Citi for refusing.
In other words, this is an escalation and a new level of Lawfare, targeting secondaries. It reminds me of one of the Rules for Radicals examples where striking workers didn't strike at their place of employment, they went to an important client of their employers and set up a picket line there, to leverage the client to give pressure to their Employer for them. It also reeks of Cancel Culture mixed with Lawfare -- "You're supporting someone we want to socially assassinate so we're going to harass you into breaking any relationships with them."
I hope this was anticipated by Trump and they have a response. Personally, I hope they black bag the bitch and in 75 years we get an FBI document dump about how they made her do a flip as they threw her out of a military plane over the Atlantic, 500 miles from the nearest landmass, but we'll see.