We are having the same issue and have a ticket open with support since 1st week of October and they still can't synchronize the NSM repository. We now have an Escalation Engineer which is working with EPS Engineer.
We have tried "Remove-SmBackup -CleanupBackups" and validated that they are still there with "Get-SmBackups".
If they can't get a resolution because its a bug and seeing that the database keeps growing and become sluggish... we will have to start performing "Remove-SmBackup".
i also was having the problem that my snapmirror snapshoots number was not show correctly. after manual refresh the number is correct. i run the Remove-SmBackup -CleanupSecondaryBackups -Confirm:$false.
so when i use remove-SmBackup -cleanupbackups this will check all primary local backups?
We ended up engaging SnapCenter Escalation and EPS Engineers which identified the issue with the snapshots accounted for in the NSM Database which were old... apparently because the Storage LIF name was changed SC can not find the path to delete these via the LIF it recorded them. They are now writing a SQL to delete these backups based on our retention policy and hopefully in the future it will be a fix.