JIRA Indexing health-check checks the state of the search index is consistent with the database. If JIRA Re-index failed for non-issue objects: comments, entities, etc and Lucene index is not consistent, it doesn't report the problem.
While re-indexing running, delete some part of Lucene data: rm -rf jira_6.4/caches/indexes/comments/*cfs
Wait for Index completes (with errors)
Run Indexing health-check,
It should report the problem.
It doesn't report the problem. JQL search is not consistent and might lead to Dashboard/filters errors.
See related https://jira.atlassian.com/browse/JRA-61577
Go to Administration > System > Indexing and check if you see error like:
JIRA is unable to perform a background re-index at this time because the index files are either missing or corrupted.