The Judge is asking them to certify that all of the material submitted in the motion to dismiss is correct. It is already known there were some errors, and there is no way the DOJ can get this done over the weekend to meet Sullivan's deadline. So the DOJ is going to have to request an extension, pushing the whole case past the election. Or maybe Sullivan tosses out the motion to dismiss due to the DOJ's failure to certify the evidence.
Perhaps the judge thinks that President Trump is going to loose. He then keeps delaying the case till after 20Jan then convicts Flynn of something. President Trump can no longer pardon him at that point.