What do you currently use for backup? Since you are using a licensed edition of vSphere, you may use any backup application. Veeam is certainly a good option.
As of ESXi 5.x it's no problem to reinstall ESXi with preserving the VMFS datastores. If you want to be absolutely save, purchase another SD card (1GB is sufficient) for the new setup, to allow you to go back to the old installation once something unexpected happens.
André