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This "reindex" works by.. doing a JIRA search for issues by filter or project, and then reindexing them. Can you spot the flaw in that scheme? Correct - if your indexes are broken to begin with, it's not going to work (and why would you be reindexing unless your indexes were broken?).
The source code, ReindexProjects.groovy is open source. I've reached out to Adaptavist and hopefully they'll incorporate my per-project reindex code.
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