JIRA administrators should pay a lot of attention to taking regular backups of data and its configurations. Luckily, JIRA comes with a handy tool to generate backups. It not only contains data (such as Issues and Projects), but it also contains JIRA configurations that are stored in the backup file, which means that when you restore the system, all the data along with various schemes for Issue Types, Workflows, will also be restored.
The backup system provided in the UI of JIRA is not much efficient when you have thousands of issues. For this, the recommended approach is to manually take a backup of your database. The details of this backup approach can be found at https://confluence.atlassian.com/display/DOC/Production+Backup+Strategy.