The point of Chesterton's fence isn't that the fence is necessarily still useful, it's that being ignorant of the usefulness of a thing isn't equivalent to knowing that it's useless.

> Go away and think. Then, when you can come back and tell me that you do see the use of it, I may allow you to destroy it.

This is the bit that applies.

Chesterton's fence is not about never changing things.

They followed Chesterton's fence to the letter. They saw something that didn't make sense, and then tracked down why it worked the way it did.

Once they understood the root cause, they examined the environment and discovered that the underlying issue had been fixed. That allowed them to confidently rework the inconvenient behavior into something better.