How does it look in the GUI? Is it really showing no Projects associated to it? How about re-indexing.
I previously had this issue and resolved it (probably more by luck than judgement) by creating a test project allocating the desired workflow. Then deleting the project. I was then able to delete the workflow scheme as it had then moved to Inactive.
I am pretty certain this would not be described as the "best answer" but it worked for me.
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