The well Mother filled in is not the same well where the completed Donkey wheel was.
Donkey Wheel well Cold Very Deep
MIB's well not cold not deep at all. They were able to use a ladder to get down to it.
3rd well is where Desmond is.
I think these wells will play a big part in the coming episodes since we know there is electromagnetism present in some wells. Widmore may be looking for them. Jack is going to rescue Desmond from a well.
Something else I found interesting was the copy of the Truce. It states digging of more than 10 feet anywhere on island would be a violation of the truce.