As a JIRA Data Center admin, the only solution to fix a Lucene Search Index consistency problem (The issue index is inconsistent with the database state. Database has (<issue-count-1>) issues but the index has (<issue-count-2>) issues.) is by either re-indexing the node or copying the index from another healthy node:
The health check should also include the option to fix the inconsistency or at least provide the list of issues affected by this problem. This would help admins to assess the best way to fix the inconsistency (e.g. using a project re-index).