After upgrading Veeam Backup and Replication to V12 you will have the option to upgrade the backup chains as well to a “true” per vm backup chain with individual metadata files. I will show you the process in my video below.
Link to upgrade Veeam Backup and Replication from V11 to V12:
https://www.vikash.nl/upgrade-veeam-backup-and-replication-v11-to-v12/
Link to Veeam Helpcenter regarding backup chains:
https://helpcenter.veeam.com/docs/backup/vsphere/backup_change_type.html?ver=120