Currently thats not supported. Multi-file addon projects right now require a retail release. I am working to support this in the future but its taking some time to rip out the legacy code that requires it on our site.
So I can remove TBC release from your classic and you can create a TBC separate project thus having separate projects for each release.
OR
Upload the classic and tbc releases to your retail project and I can delete the Skillet-Classic project.
Let me know what you'd like to do