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One advantage of the Microsoft Application Virtualization (App-V) Sequencer is the capability of running via the command line This allows for automating the sequencing of applications which do not require any special customizations in their guidelines or "recipes" for sequencing. The upgrading of a package can also be automated using the command line sequencer.

The documentation for upgrading a package can be found here:

http://technet.microsoft.com/en-us/library/cc843768.aspx

In addition to the above reference, here are some other tips you might find helpful:

UPGRADE and OUTPUTFILE Must be Different

The command line sequencer will not update a package if the source path specified in the /UPGRADE switch is the same as the path in the /OUTPUTFILE switch. This will throw a sharing violation error.

DECODEPATH must be specified

Remember the Upgrade option is the same as a "Package Upgrade" or "Opening a Package for Upgrade" in the GUI version. This means the package has to be decoded into the mount\VFS path.

OUTPUTFILE location needs to be on a separate drive as one specified in the DECODEPATH option.

INSTALLPACKAGE Options: 

If the update is anything other than a standard MSI, it is recommended to contain it with a batch file or script. The command line sequencer should be able to grab everything even if it is a simple file copy or registry import.

Hope this helps,

Steve Thomas | Senior Support Escalation Engineer

The App-V Team blog: http://blogs.technet.com/appv/
The WSUS Support Team blog: http://blogs.technet.com/sus/
The SCMDM Support Team blog: http://blogs.technet.com/mdm/
The ConfigMgr Support Team blog: http://blogs.technet.com/configurationmgr/
The OpsMgr Support Team blog: http://blogs.technet.com/operationsmgr/
The SCVMM Team blog: http://blogs.technet.com/scvmm/
The MED-V Team blog: http://blogs.technet.com/medv/
The DPM Team blog: http://blogs.technet.com/dpm/
The OOB Support Team blog: http://blogs.technet.com/oob/
The Opalis Team blog: http://blogs.technet.com/opalis