Upgrading to BE 2010 R3

Upgrade from Backup Exec 2010 to Backup Exec 2010 R3 will keep all your current jobs, settings, selections, schedules, catalogs, licenses, etc

Post successful upgrade you will however also need to:

a. Run Live update a couple of times to make sure Backup Exec 2010 R3 is fully patched with the latest service pack and/or hotfix

b. Re-install all Remote Agents for Windows System (on remote machines)

Also, i'd recommend a little precaution before you begin upgrade - Backup the current Data and Catalogs folder.
1. Go to services console and Stop alll Backup Exec services (including the SQL service)
2. Go to the Backup Exec install directory (usually C:\Program Files\Symantec\Backup Exec)
3. Locate and Copy following two folders from the above location:
        - Data
        - Catalogs
4. Paste them on a different location (like different volume/machine) as a backup.