Read the changelog: https://www.apantic.com/products/minesync.10/changelog
Estimated Upgrade Time: Less than 10 minutes
There were no major changes in 2.0-beta.2 -> 2.0-beta.3 that would require significant manual intervention.
The config.yml file was not changed.
A few more XF options have been added. You can view these by going to XF Options -> [A] MineSync
There are no important upgrade notes. You will be able to upgrade normally, by replacing the .jar with the 2.0-beta.3 JAR on your server, and doing a regular file upload + xml upgrade in the XenForo end.
If you have any troubles or any further queries, please contact our support team.