SCCM 2012 is unable to unpublish applications successfully when folder redirection of the AppData folder is enabled.
The appenforce.log file will display the following error messages:
Unpublish-AppvClientPackage : Application Virtualization Service failed to
complete requested operation.
Operation attempted: Unpublish AppV Package.
Windows Error: 0x78 – This function is not supported on this system
Error module: Catalog. Internal error detail: 86B0572600000078.
Please consult AppV Client Event Log for more details.
At line:1 char:106
+ import-module ‘C:\Program Files\Microsoft Application
Virtualization\Client\Appv …
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~
+ CategoryInfo : InvalidResult: (:) [Unpublish-AppvClientPackage]
, ClientException
+ FullyQualifiedErrorId : UnpublishPackageError,Microsoft.AppV.AppvClientP
owerShell.UnpublishAppvPackage
An updated version of the application is then unable to install correctly until the application is removed correctly. To achieve this I had to manually remove the package folder from the APPDATA\Roaming\Microsoft\AppV\Client\Catalogs\Package\{Package ID} folder.
App-V5 SP2 will address folder redirection issues and hopefully this problem will therefore be resolved at the same time. Once SP2 is released I will update to confirm the news.
SCCMentor - Paul Winstanley 
Tim Mangan was kind enough to allow me permission to post his opinion on this topic. Thanks Tim!
“This is a work in progress. We do not yet know what the final SP2 release will do, but can hope that the app-v client would use impersonation when needed.
That said, blindly redirecting all of AppData tends to be a bad idea, so redirection at a lower level might be a better idea. Since SCCM is in play, I am guessing that non-persistent VDI is not being used, so only redirecting what must be saved for system rebuild is probably a good idea. Giving the local system permissions on the redirected folders is an easy way to go for now, and although security minded people might object it is not really all that risky (the same locations are writable by the computer account if you didn’t redirect) – you just must be aware that in the case of infection you must do more than just wipe out the local machine.”