Something is definitely fishy here, and my Elasticsearch senses are tingling.
Can I recommend that you try the following (this will result in some downtime)
- Stop your SonarQube server
- Fully remove the data/es6 folder in your SonarQube install directory
- Start your SonarQube server
SonarQube data will be reindexed – this often solves discrepancies like what you’re observing.