So move/merge the locations since that is clearly the intention if the user has a redirection setup. A simple message confirming that "there are 2 Documents folders and would you like to move them to a single location" would be sufficient.
This is just a project management failure that somehow got through, but the fact that it did seems to show major QA issues.
Merging the locations can easily get complicated. What if the same file exists in both folders? What if it exists in both folders, but with different contents? What if not only it has different contents, but also the same last modification time?
Why is it complicated? It's no different than moving any other folder to a new location which already has one with the same name, something that has been handled for decades now.
It should be the same exact action, just triggered by a message saying "Documents folder detected in 2 locations, click OK to copy".
This is just a project management failure that somehow got through, but the fact that it did seems to show major QA issues.