The issue might occur in the following steps.

1. Back up a virtual machine. (At this time, the only used space is backed up.)
2. Create the template of the virtual machine.
3. Deploy the new virtual machine from the template.
4. Back up the deployed virtual machine. (At this time, the entire size of VMDK file is backed up.)

[VMware KB regarding "Unknown change epoch" in Hostd.log]
http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1033816

Recreate the VMDK descriptor file with reference to VMware KB 1002511 and back up the virtual machine.

Recreating a missing virtual machine disk (VMDK) descriptor file
https://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1002511

Applies To

ESXi 5.0 with vCenter

The entire size of VMDK file is backed up when backing up a virtual machine of thin provisioned type that was deployed from VMware template.

The following lines might be found in Beremote debug log and hostd.log on ESX.

[Beremote debug log]
[5404] 07/30/12 19:05:50 [fsys\vmvcb] - VM_VCBPROXY_FS::GetFirstDiskChangeInfo() Node name: 'DiskChangeInfoResult' offset Length: [(0):(8589934592)][(0)+(16777216)=(16777216)]
[5404] 07/30/12 19:05:50 [fsys\vmvcb] - VM_VCBPROXY_FS::GetFirstDiskChangeInfoExtent() Node name: 'ChangeArea' offset Length: [(0):(8589934592)][(0)+(16777216)=(16777216)]
[5404] 07/30/12 19:05:50 [fsys\vmvcb] - VM_VCBPROXY_FS::GetFirstDiskChangeInfo() Node name: 'DiskChangeInfoResult' offset Length: [(0):(8589934592)][(0)+(16777216)=(16777216)]
[5404] 07/30/12 19:05:50 [fsys\vmvcb] - VM_VCBPROXY_FS::GetFirstDiskChangeInfoExtent() Node name: 'ChangeArea' offset Length: [(0):(8589934592)][(0)+(16777216)=(16777216)] [Hostd.log]
2012-07-30T19:05:23.661Z [709D6B90 error 'vm:/vmfs/volumes/xxxxxxxx-xxxxxxxx-xxxx-xxxxxxxxxxxx/Deployed-from-Template/DeployedVirtualMachine1.vmx' opID=e2a967bf-4e] Cannot compute changes for disk /vmfs/volumes/xxxxxxxx-xxxxxxxx-xxxx-xxxxxxxxxxxx/Deployed-from-Template/DeployedVirtualMachine1: Unknown change epoch.