We have ScriptRunner available, if it helps. We're trying to find issues that are:
In other words, my current search returns an issue that is "blocked" but the blocking item is done. In this case, I don't consider the issue to be blocked anymore because the blocker is Done.
issueFunction in hasLinks("is blocked by") or issueFunction in hasLinks("blocks")
So, I think you're about half way there. The hasLinks JQL function provided by scriptrunner can help you find those issues. But you then also need to lookup the status of those linked issues to be able to make sure you don't include blocked issues that are already in a status of "Done". Fortunately, it looks like scriptrunner does have another function called linkedIssueOf that can help here.
(issueFunction in hasLinks("is blocked by") AND issueFunction in linkedIssuesOf("status != Done", "blocks")) OR (issueFunction in hasLinks("blocks") AND issueFunction in linkedIssuesOf("status != Done", "is blocked by"))
I think that this JQL query, with scriptrunner of course, can help with locating the issues you are wanting to see here.
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