The 48 empty folders are intriguing. My initial reaction is "The SOB gave them away or he's still hiding them somewhere" but it's hard to say without knowing more.
Based on what I've read in various media reports, the government keeps an inventory of some sort to track documents, so they may be able to determine if the contents of empty folders have been returned. That's speculative though, I really don't know.
If the documents are still unaccounted for, it could put the DOJ in a somewhat awkward position. Trump could decide he has an incentive to keep hiding the documents on the theory that turning them over would be an admission of further guilt. In theory the government could offer immunity against additional liability if he comes clean and returns any documents he still has, but the government might not have any way to know if he really did come clean (e.g. how would the government knnow he didn't copy some of the documents before returning the originals). To date, his track record with regards to coming clean is unimpressive, to say the least. On the other hand, a series of searches of Trump's other properties that turn up nothing would obviously give Trump a big talking point (of course it's not at all clear the FBI has sources outside of Mar-a-Lago sufficient to demonstrate probable cause even if Trump has hidden documents in other locations).
>>>WASHINGTON — The F.B.I.’s search of former President Donald J. Trump’s Florida club and residence last month turned up 48 empty folders marked as containing classified information, a newly disclosed court filing shows, raising the question of whether the government had fully recovered the documents or any remain missing.<<<
A detailed inventory of items seized in the F.B.I.’s search of Mar-a-Lago raised the question of whether the government had fully recovered the documents or any remained missing.