The short answer is "everything should be OK".
You can look at the target VM and there should be a couple of snapshots created by Converter - "backup" and "bootable" snapshots with a timestamp. At the end of each cloning task Converter creates a couple of snapshots - the first one is the "clean" state of the source, the second one is after applying "configuration" changes to make the target bootable. When another synchronization run is started, the target VM is reverted back to the "backup" snapshot and incremental updating starts from there.