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It seems that you cannot remove all of the subject associations from a database record. We've reported this to Springshare.
Springshare was already aware of this bug, and there is a path that will be pushed live sometime in June. I'll update once the problem has been fixed.
You can now remove all subject associations from a database record.
This issue was reported on 5/29/15 and resolved on 1/20/16.
Written by Jon Earley, Jon Bloom, and Matthew Reidsma for Grand Valley State University Libraries. Code is available on Github.