Whenever there is an issue with the instance, any experienced JIRA administrator will always have an idea of where to look first to fix these problems; however, there is a built-in tool called Integrity Checker that can be used to identify any possible problems. Perform these steps to use Integrity Checker tool:
Go to Administration | System | Integrity Checker (under TROUBLESHOOTING AND SUPPORT).
Check the Select All checkbox:
Click on the Check button to continue:
On the next screen, the system will display the list of problems with the configurations found in the instance. You can check the Fix All checkbox and click on the Fix button to resolve these issues. Alternatively, if you know the actual reason behind these problems, you can resolve them manually and run Integrity Checker again.