So are they trying to claim that Trump hid classified records in files marked as unclassified?
If so, then this issue of them “misplacing” means that they almost certainly did what they are accusing Trump of doing.
That seems to be the size of it.
I think the Trump team, when they said “There are no photographs or logs documenting the nature in which the allegedly classified documents were commingled with personal effects..." and "the evidence ”was materially exculpatory,” was alleging that the fact that documents marked classified were packed along with personal items means that President Trump had declassified those documents according to the Presidential Records Act and had them stored along with his other personal effects.
By changing the order of documents and potentially moving classified documents to boxes that contained no personal effects because they didn't know which documents went with which placeholders, the exculpatory nature of commingled documents is no longer there.
-PJ