Make sure that you are on Refined for Jira version 2.0.10 or later. If not, please upgrade to version 2.0.10 before you upgrade or 2.1.10 before upgrading to 3.0.x.
Go to Manage apps and find Refined in the list of installed apps. If you're not on the latest version, you should see a button to upgrade to the latest version. Click on the upgrade button.
If you're not on the latest version and you don't see the Upgrade button, you can always download the JAR file from the Atlassian Martketplace.
Once you have upgraded to the latest version, click on the Get started button. If you don't see the Get started button, you can navigate to the Refined administration using the link in the left navigation bar of Jira.
In the Refined administration page, you should see a button prompting to Upgrade the data. Click on the Upgrade button to finish the migration of data. You can now continue to use Refined.