Nevermind. I figured it out.
I like to run everything as services so service starts and stops are handled automatically and gracefully without logins.
I had set many services to have drivepool dependency that stored data on the drivepool.
MSI installer doesn't know how to handle the depency even though the service is not restarted till reboot?
Anyways, removing drivepool dependencies allowed the update to finish installing.
Is it possible for the MSI updater to handle drivepool dependencies so that I don't have to remove them every update?
Scuro's post in Can't Update DrivePool was marked as the answer