I've got a VERY strange behavior here. One workflow, which is in fact inactive/not assigned to any workflow scheme, cannot be removed, because JIRA locks it as active. Any ideas, why this happens? See the screenshots for more details.
Try running an integrity check.
There could be some issue associations that weren't cleaned up correct. If that doesn't help give us a holler at support.atlassian.com so we can take a look at your logs and see what's going on.
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