You can delete backups with the prlctl backup-delete command.
To delete a specific VM or container backup, provide the VM or container name or UUID as well as the backup ID (you can find out these IDs with the prlctl backup-list command). For example:
# prlctl backup-list ID Backup_ID Node Date Type Size {c1dee22f...} {209d54a0...} test.com 2011-05-30 10:19:32 f 411566405 [The ID and Backup ID are reduced for better readability.] # prlctl backup-delete MyVM -t 209d54a0-e3b8-4a03-9ca8-d4cc7a2a27ca --keep-chain
With the --keep-chain option specified, the remaining backup chain will be preserved after specific backups are deleted from it.
To delete all backups of a VM or container, specify only the VM or container name or UUID:
# prlctl backup-delete MyVM