When the App-V sequencer creates a GUID for the package that needs to be unique. If somehow two packages get the same GUID, you will run into an error at deployment and need to re-sequence.
In older releases, people would run into this issue if they took a VM snapshot with the sequencer up and running. Typically, they create the VM, install the sequencer launch it and then take the snapshot. A long time ago, this GUID was generated when the sequencer started, so the snapshot captured it and you got a duplicate. Then Microsoft changed the GUID to be generated when you started the sequence, so as long as you didn’t do the “file new” before the snapshot you were OK.
It seems that Microsoft has changed how and when this GUID is generated in 4.6. I ran into this in my lab this week and traced it down.
Normally, I take a VM snapshot without the sequencer, and then a second with the sequencer installed but not running (old habbits die hard). But this week I have been reverting to the VM without sequencer, installing it and sequencing each time. At the end of the sequencer install is an option to launch the sequencer from the installer. It appears that if you use this option the Package GUID you get will be duplicated, if you revert the VM, install the sequencer and have the sequencer installer launch the sequencer. For detail, even though the package GUID is duplicated, the package version GUID is different.
I verified that not having the installer launch the sequencer solves the issue, your package gets a different GUID. So you are forwarned: