I'm sure our tech support team has a working solution for you. There are multiple workarounds for the issue, unfortunately the way SCOM works there always could be orphaned objects in the system. Once discovery removes them - the issue should be gone, but could occur again and again.
We really want to find a permanent solution for the issue, we already have some thoughts on how to fix symptoms of orphaned objects - errors about accessing Veeam logs, but what we really would like more is a solution for the root cause. And for that we need to understand all possible ways to produce orphaned objects - it's not that easy to create an orphaned object, but in some environments they appear&disappear, again and again quite often. We need to understand why.
Could you tell us more about your environment? Common reason for orphaned objects is frequent removals of VMs without SCOM agent uninstallation, do you have something similar? VDI(Vmware View)? Also sometimes VMs could frequently migrate from unmonitored hosts to monitored hosts and vice versa, do you have something like this in your environment?
We would really appreciate such additional information. You can tell us in a private message or using the support ticket.