Unless you are running Microsoft Cluster services, and with VMware HA I'm not sure why you would, I can't really see a reason not to thin provision. However, as capacity within the guest is consumed, the size of the VMDK files increases. Even once data is cleaned up, that VMDK space is never reclaimed. Virtual Center shows this as "Provisioned Storage" vs "Used Storage" as shown in the screen shot below.
In this case the VMDK is 16GB and I'm currently using 13.18GB on disk. When we take a look at the host we can see it has only a couple of GB consumed.
# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/rootvg-root 12G 1.9G 9.3G 17% /
tmpfs 499M 0 499M 0% /dev/shm
/dev/sda1 95M 43M 48M 47% /boot
/dev/mapper/rootvg-var 2.0G 117M 1.8G 7% /var
The easiest way I know to fix the problem is to storage vmotion the guest to another datastore and after, if you like, to move it back. The trick is, you have to zero out the extra space in the file system first in order for vmware to thin provision it.
This is pretty easy, although it can take a few minutes depending on how much space you need to 'fill'. The following will create a 9GB zero filled file, flush changes to disk, and then remove it. You could of course fill the entire file system but this could impact running applications, so I'll leave that up to you to decide.
# dd if=/dev/zero of=/fill_file bs=1024k count=9216; sync; rm /fill_file
Now your free space in the virtual disk is filled with zeros. All that's left is to storage vmotion the VMDK to another datastore. I only have experience with NFS, in which case I can selece "Same format as source", if you are using VMFS you should probably select "Thin provisioned format".
Once completed you'll see the used capacity back in line with what the host is actually using.
