I think it does nothing at all.
According to the hintbook it used to do something in the past of Terra, but not anymore by the time the story is happening.
Also, not a single walkthrough or fan page on the internet does have any information about the well. So I suppose there are 3 possibilities:
a) a bug that renders the well functionless
b) it was never intended to do something
c) or the puzzle to get it to work is that complicated no one could figure it out
Thanks for response. I think it could be that it was meant to do something, but the quest was not completed and did not make it to the final game. Maybe it was done on purpose to keep the players guessing what's going on...