Hi,
the trick is in the Application configuration Step during Sequencing.
When you are there, you see the list of applications that the sequencers recognized. Here you can modify for instance the Name or Version of "Cue" to something like: name: "Cue"; Version "WebPremium+Original Version number".
The Rule:
"The Combination of Name and Version has to be unique for an App-V evironment."
Users only see the "version" information when the App is loaded, so it does not appear on the shortcut.
Of course you also could modify the version info for Cue within Indesign.
If you aren't experienced with OSD file Modification, it is the best you re-open "For Package Upgrade" one of the Packages on the Sequencer and go through the Sequencing Wizard again until you come to the App Configuration Step (you don't have to install anything new)...