First, if you just replace the file in /data/ that won't do anything. There is a way to make that work, but I don't recommend it because it creates other errors.

Second, I've not been able to do this myself. I THINK it's the problem I described here https://forums.elementalgame.com/394013 after James009D pointed out the issue. Specifically,

Since <tiledesignobject> tag can clearly be stacked, I think we can't do anything about it at the moment. You can either google how to make a new data.zip or wait for a fix.

One way around this is to add an unachievable prereq to the original tile so that it's permanently unavailable then create a duplicate of the original xml data referencing your new tile.

EDIT: I've not done this particular thing myself but i've been using similar rule bending for other things. I have a feeling you may have to create a "fake" tech in the tech tree that's never researched and use that as the prerequisite.

Of course, even if this works it's a really clunky way of doing things and hopefully this duplication problem will go away soon.

EDIT2: I used this kind of thing to stop huts auto upgrading to houses by making the huts upgrade to a fake house. I prevented my fake house appearing by using;

    <Prereq>
      <Type>Tech</Type>
      <Attribute>NULL</Attribute>
      <Value>0</Value>
    </Prereq>

So a fake tech isn't required in the tech tree.