I finally found the solution. It took me longer than I expected. It was a caching issue.

• First, go to the project in Finder and right-click the .xcodeproj.
• Press Inspect Package Contents, and delete xcuserdata inside it. You don't need to delete xcshareddata.
• You'll also see project.xcworkspace. Do the same for that, too. And the warning goes away. Yay!