Ok. Thanks for the information.
IF you were given permission to keep the well despite the rule, then you should be able to claim your right to continue to use the well IF you can prove that this permission was granted.
Hopefully, the board put something in its minutes to reflect that you were given permission to keep the well. You should review the meeting minutes to see if there's anything in there. Also, IF you can have the board member/s who gave you permission to provide the new board with an affidavit stating that you were allowed a variance on the policy and that the well was accepted by the board, then you could argue that this is adequate authority for you to keep the well.
If there is nothing in the minutes, that's very harmful for you, and if you can't get an affidavit, etc., then that's probably fatal to your claim.
I also considered a claim that it's been there long enough to grandfather you in, but I don't think that is a legally sound argument because (1) the rule was in place when you dug the well (to be grandfathered, you would have had to dig the well BEFORE the rule was in place) and (2) because this is a continuous violation of the rules, the statute of limitation starts over every second.
So, your best bet is going to be IF you find minutes or get an affidavit from the previous board member/s. If that can't be done, and there's no proof of permission, you're likely going to be forced to cap the well, unfortunately.
Maybe you can work out some type of agreement/settlement with the HOA that will allow you to keep it. However, that's going to depend on how negotiable the HOA wants to be.
I'm sorry the news isn't better, but I'm only trying to be honest about the situation
and the law that applies.