I updated my Xcode to version 8 after iOS 10 release. Apple made some changes in code signing process and it is now available in general section of target settings. But the
I faced the same issue, fixed it without having to delete and download everything again.
I simply enabled Automatic Signing, waited for it to detect my signing certificates, and then disabled it. After that, I was able to reselect the desired provisioning profiles and the Signing Certificated were detected as they should.