In order to resolve the issue perform the following steps:
1. Stop Veeam Backup Enterprise Manager service
2. Run the SQL script against VeeamBackupReporting database using SQL Server Management Studio:
UPDATE [dbo].[Repl.Topology.BackupDbInstances]
SET [last_sync_usn] = 0
FROM [dbo].[Repl.Topology.BackupDbInstances] INNER JOIN [dbo].[Repl.Topology.BackupServers] ON [dbo].[Repl.Topology.BackupDbInstances].[id] = [dbo].[Repl.Topology.BackupServers].[current_db_id]
WHERE [dbo].[Repl.Topology.BackupServers].[ip_or_dns_name] IN ('ADDED_BACKUP_SRV_NAME1', 'ADDED_BACKUP_SRV_NAME2', …)
Make sure to replace the ADDED_BACKUP_SRV_NAMEi parameter with the name of your backup server.
3. Start Veeam Backup Enterprise Manager service, all jobs will be added to Enterprise Manager on the next collection