I did a host reboot and it looks like it wiped out the verticalbackup folder in the /opt directory. Is there a way to prevent this that you know of?
You can install the vertical executable to a datastore directory which should persist after a reboot.
I reported this a while back. Don’t you think it would be wise to update the guide? 
Sorry about that. I was meant to first figure out which version (5.5, 6.0, and 6.5) of ESXi would wipe out the /opt directory after a reboot and then give a definitive guide on where to put the executable. This is taking some time so I haven’t updated the guide yet. Should be done in this week.
All versions of ESXi wipe out everything but datastores. I believe they have a semi-official extension mechanism (https://pubs.vmware.com/vsphere-4-esx-vcenter/index.jsp?topic=/com.vmware.vsphere.installclassic.doc_41/install/extensions/c_extensions_container.html) that allows things to stay, but otherwise installation has to be on a datastore.
Just put your files in “verticalbackup” directory on a datastore. It is what other backup programs suggest, and it works for me for verticalbackup.
@gchen, I do suggest updating the guide with this, I had this same problem. Since the guide suggested /opt and I wasn’t familiar with esxi at the time, I thought this implied that it would persist. It didn’t.