Don't know the time/score situation, but, I believe I would stop the clocks (if the game clock is not already stopped), take the time needed to retrieve the ball and get it spotted, set the play clock to 40 after we get the ball spotted, and then resume the game. If either team complains, let them know that you must have ball persons for both teams on BOTH sidelines, with a replacement ball(s) for their respective teams at all times, if they want you to manage the game more expediently. Otherwise, carry on retrieving and spotting game balls with the clocks stopped. If the uncooperative coach loses the game because his opponent got a full 40 seconds for each down, with the game clock running late in the game, maybe he'll be more cooperative in the future.
For those playing NCAA rules, the use of the 40-second play clock was predicated on the ability of game officials to spot the ball expediently. That is a non-issue for FBS/FCS/D2 and D3 games. They provide appropriate ball persons, and replacement game balls.
With those athletic organizations that use NCAA rules but don't control their member institutions to the point that they provide the necessary resources to manage the game as intended, the Referee will have to exercise his authority and do what it takes to manage the game fairly. Yeah, he could 'pump' the play clock to 25 for each down that takes longer than that to get the ball spotted, but that would still not allow teams to run the fast-pace no-huddle offenses that the 40-second play clock generated, and to which the teams are entitled. In exchange for this process slowing them down, allowing them the full 40-seconds to make their subs and make their play call AFTER the ball is spotted isn't unreasonable. Yeah, it adds real time to the game, but this kind of game ain't gonna be 'governed' by TV time constraints, anyway.