Virtual machines with LVM partitions inside cannot be compacted. The compacting command finishes successfully, but the disk size remains the same from the node's perspective.
[root@vz ~]# prl_disk_tool compact --hdd /var/parallels/testvm.pvm/harddisk.hdd Operation progress 100 %
/var/log/parallels.log the following error is logged
F /imagetool:838351:838351/ Failed to get FS bitmap for partition 2 . error (7|1). Skipped.
Compacting functionality for virtual machines with LVM partitions is not implemented in current version of Virtuozzo.
The issue will be fixed in scope of the feature request PSBM-3730.