Since SCOM does not remove the entries automatically, you will need to remove them manually.
1. Clean Veeam Run As Profile for vCenter Connection Failover.
2. Export the Microsoft.SystemCenter.SecureReferenceOverride MP as .xml.
Make a backup of the exported .xml so that you can revert to it if needed.
4. Edit the .xml in Notepad and locate the following block:
Note, that the version may vary based on the build of Veeam MP you are running.
5. Remove this block.
6. Save the updated .xml and import it into SCOM.
7. Remove Veeam MP.