You should be fine, as long as you leave the "VMFS" partitions alone. I don't believe the partition tool (don't remember name) knows about specific versions of partitions so it just says VMFS.
You should see your partitions when you are done installing.
So as long as I reinstall leaving the VMFS partition alone and then let it boot into ESX, I should be okay then? Is the only way to verify the VMFS version in the VIC in the configuration under storage? Any CLI to verify VMFS partition version? I just want to make sure that when I walk away from this project that everything is going to be fine. Thanks.
If you install VI3 and you have a v2 VMFS you will have the opportunity to upgrade to VMFS3 in the client. There may be some compatibility issues with running a v2 datastore on v3 OS, check the forums. The upgrade from VMFS2->3 is non-destructive.
If you have console access to your VMFS partition you can check its version using this command:
vmkfstools -P (datastore name)
the "p" is capital. The output should look something like this:
\[root@waprdbrvmwh01 volumes]# vmkfstools -P VMotion2
VMFS-3.21 file system spanning 1 partitions.
File system label (if any): VMotion2
Capacity 599953244160 (572160 file blocks * 1048576), 123554758656 (117831 blocks) avail