Hi Anatoliy, if you're using vCenter Server connection for your backup jobs, then it doesn't matter where your VMs are located. For example, if you're using folders, then all VMs from the folder will be backed up. On the other hand, if you're adding VMs explicitly to the backup job, then it doesn't matter what location they currently have, as the backup job will query vCenter Server for VM location and then will start backing it up.
P.S. please be aware that the logic above does not apply to the situation when you re-register VMs in the inventory. For more info on this topic, please check out this thread > Moving VMs to a new virtual center.