A question that's a duplicate of another question should be marked as such.
This is true even if the two questions have been answered differently. (In some cases, two questions can actually be merged so that the result is a single question that contains all of the answers from the original two combined.)
However, it's incorrect to assume that there is an exact 1-1 correspondence between questions and answers. In other words, while duplicate questions may lead to the same answer, it doesn't work that way in reverse.
Duplicate answers don't always lead back to the same question.
It's quite possible to have two different questions, both of which can be answered in the same way.
Q: What colour is used by most stop lights to signify "stop"?
Q: What is the colour of the maple leaf on the Canadian flag?
Here, these questions are most certainly not duplicates of each other despite the fact that their answers are identical.
Although this is a simplified example, I am sure there are some situations where different questions can be answered by identical answers of a more complex nature.
In the scenario presented in the question asked here, the answer for one question was deleted because it was used as the answer for another question. The reasoning given was that using the same answer for two questions is disallowed.
However, as per the example above, this makes little sense. When two clearly different questions actually do have the same answer, then that answer should be allowed in both places.
In fact, even that is a moot point—because even incorrect answers are normally allowed to remain.
I'm not aware of any policy that says "bad answers" (aside from those that violate codes of conduct) should be deleted. It's actually the point of these sites to not do that—and to let the community judge an answer's validity through comments and votes. (Just look at the number of questions posed on this site that complain about bad answers—and the continuing decision that that they should remain.)
If the questions in this case are actually duplicates, then one of them should be marked as such. But if they aren't duplicates, then the answer should have been allowed to stand in both locations.
If something entirely different was going on in this case, then that hasn't been made clear from the details provided, and we need more information before being able to make an informed judgment. For instance, links to each question and an indication of the answer that was deleted from one of them—along with the actual reason stated for the deletion.