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Which files a/o directories should I be looking at?

Which files a/o directories should I be looking at?

I used an add-on tool to edit the order of titles in the main left-hand Nav Bar. Now I have two copies of the Nav Bar, both in the same column, one over the other. Editing entries from within Magento edits the top one while the add-on tool edits the lower one. To make matters worse they don't look the same.  The top one (the one I think I want to keep) has a light blue background with dark blue lettering.  The bottom one (the one I think I want to delete) has the original colors.

 

Which files a/o directories should I be looking at?