Due to an uncompleted migration in a version before 6, it could happen that sets in the configuration get duplicated. With version 6 we included a process to automatically resolve those.
The page to trigger the deduplication can be found under:
By pressing the button, it will look for a set, that is duplicated and merge them together. In a second step it will then manipulate the dropdowns on pages that were linked to the 'wrong' set.
Before using this process, please make sure that the instance is indexed and that you have done a snapshot.