Pretty sure the entirety of the documents seized in the search, minus a handful of personal items that were returned to Trump immediately after the search (e.g. passports), remain in FBI (or at least more broadly Justice Department) custody. The confidential/secret marked files were supposed to be available for review at a secure facility there in Florida, held separately from the boxes of all other documents.
Even Trump's Cannon agreed & ordered (back in 2023) that the classified documents "are now and will remain the property of the United States." The order terminating the case did not make any mention of the documents, other than "This Order shall not affect or weaken any of the protections for classified information imposed in this case or any protective orders pertaining to classified information"