All files for my workspace appear twice in the Project Navigator (Xcode 9.4.1) but if I delete one from the project (only deleting the reference), both disappear and if I add a file it gets added twice.
I have not found a question with the same issue. I may have to create a complete new workspace but I would like to avoid that.
This post is similar: Duplicate target after "pod install"
In Finder, if you Show package contents of your .xcworkspace file and then view contents.xcworkspacedata, you'll see a duplicate in that file.
To fix, delete your .xcworkspace, podfile.lock and pods folder and do "pod install" again...