Who, exactly, has ‘jurisdiction’ if a Federal Court doesn’t?
The federal court that granted the warrant in the first place is the one with jurisdiction. Instituting a separate civil lawsuit over the scope or execution of a warrant was very unusual. And the court of appeals determined that the second federal court did not have jurisdiction over a case already in a different federal court.
Realistically, Trump's lawsuit was a huge longshot.
Federal courts are courts of limited jurisdiction. They only have the jurisdiction specifically granted to them by statute and the Constitution. There is no statute giving a district court the jurisdiction to hear Trump's lawsuit.
Trump's lawsuit relied on a series of lower-court cases recognizing an "exceptional," "anomalous" form of equitable jurisdiction to order the government to return property seized under a search warrant before any indictment. The 11st Circuit held that the factors courts have held necessary to support such jurisdiction were absent here.