I know this thread is about 2 weeks old, but it seems like nobody has yet found a solution to this problem and I find this topic very important as well as interesting.
From my experience, there are multiple ways to remove/edit the name of a rank. However, I feel the best way to do this would be by MANUALLY doing it.
In essence, follow the steps below I have laid out for you.
PART 1
1. Turn your server off. 2. Make sure it is completely off. 3. Now that it died, go to your "properties" folder, and open up ranks.properties. Note: You can open Windows Notepad first, and then drag the file(ranks.properties) onto the window; this will open the file in notepad. 4. Remove or Change the name of the duplicate rank to whatever you want. 5. PLEASE...remember to press save. (File > Save)
PART 2
1. Launch Server 2. Enjoy no more duplicated ranks.
Pers. Commentary
Spoiler:
I think I had found this solution in 2012; I really have no clear memory though.
Note: The Developer(s) of MCDzienny have resigned and the software is no longer supported. Errors are bound to occur and Mojang has not attempted to resolve them.
Basically the system does a "defense check" meaning it rebuilds itself if it finds anything wrong or out of place and so prevents any attempt to remove any essential parts(default ranks).
Spoiler:
totally portability
^I call that the antivirus 'false' alarm.
Spoiler:
Just an Ex: Windows Task Scheduler = Never stop running(rebuilding) "Something that keeps on running no matter what you do to try to stop it"
To Fix?
You are allowed to create another rank called SuperOp...but you can't remove it. What does this mean?
It means it doesn't check whether or not there is already a SuperOp rank created(that's the fix).
Note: The Developer(s) of MCDzienny have resigned and the software is no longer supported. Errors are bound to occur and Mojang has not attempted to resolve them.