But the middle stump was not out of the ground
I don't understand your scenario? The middle stump was knocked over, yes?
This actually happened
In Oz, we (used to anyway) play 2-day grade matches on consecutive Saturdays
Our team batted first on an absolute belter leaving the opposition to chase the following week
In those days, it was usually left to a couple of volunteers to put the covers on as the ground staff finished up at about 3 pm
Couple of our guys arrived to find 2 pitches marked up side-by-side, "guessed wrong" and covered the wrong pitch
As luck would have it, it poured down with rain that night leaving the match pitch saturated down one side as the covers were not big enough to protect all areas
The day itself was perfectly fine with play possible
What should the umpires do?
This sounds like a local playing conditions issue; since the Laws aren't set out with 2 day games with a week interval in between in mind.
The umpires duties under Law 3 are simply to ensure conditions are fit for play. The use of covers is the duty of the grounds staff under Law 11. The actual playing surface itself is not to be covered overnight, except in the case of inclement weather.
The laws do allow for the playing surface to be changed during a game, provide the Umpires and Captains are all in agreement (Law 7.4), but thats only if they all agree it's 'dangerous or unreasonable for play to continue on it'
So my answer would be that if the original pitch was now significantly harder to bat on compared to the first innings, but the pitch that was 'accidentally' covered overnight is closer in nature to it, then provided all parties are in agreement, a case could be made for changing the pitch for the second innings. However, if the pitch is only slightly more damp than the previous innings, and the covered strip is too different in nature, then unfortunately the side batting second would just have to cop it and move on. A note could be raised with the local regulatory board and with the groundstaff, and action could be taken to prevent it from happening again, but yea tough luck.
there is a fielder on the rope running from fine leg to deep square to save a rolling boundary on a windy day
he puts in a big thunder dive to stop the ball and comes up short, but due to the wind his hat flies off
it lands in the path of the ball
the ball comes to rest in the hat short of the rope
what do you call
Let play continue. It was an unintentional event; you treat it the same as you would treat a ball hitting the non-striker's stumps or the umpire. Just bad luck.