If everything is working now to your satisfaction, then I would leave it as-is unless you just want to clean up the UI folder. For players with a similar situation who may come to this thread for info, I'll show you a way to differentiate between custom UIs in the /loadui window.
In each of your three DarqUI folders, there is a file called
eq2ui_skininfo.xml. This file can be opened in Notepad, and it contains the UI description that appears in the /loadui window.
Open eq2ui_skininfo.xml in each folder and find
text="DarqUI Unified". Change the text between the double-quotes to something unique like "DarqUI v3129" (see image). After you have changed at least two of the three skininfo files, type /loadui in-game and you'll be able to see which copy has all of your settings.
Now you only need to do two more things: 1) On the Files page of the utility, make sure the Custom UI folder line is pointing to the correct folder (hit Browse if you need to change it), then 2) move or delete the other two folders from \UI.
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