My personal feeling is that the incorrect count would need to have been "appealed" before the start of the next hand. It's an unfortunate situation, but I think it's ultimately up to the player to be counting the chips with the dealer (and in this case the floor) in order to verify the count, during the count. Players at the table interested in seeing a person eliminated should have also stepped in and corrected the dealer or floor if the incorrect amount of chips were being pushed. Because we are into the next hand, I think it is too late and I would rule that the play stands, IMO.
One other thing - can we be absolutely sure that the floorman actually did take 5000 less than he was supposed to, or is he relying on the winner's statement that he is missing 5000? If there is no way to verify the loser's original balance, I would hesitate to take back the 4000 now given that the winner could simply hide a 5000 chip and lie, claiming he was shortchanged.