This article will deal with issues with pinning shortcuts to the taskbar that are virtualized with SWV/SWS
When pinning applications like chrome to the taskbar and you disable the layer and then upgrade the package to a new version the icon turns to a white paper and is unusable.
When it comes to pinning applications to the task bar, this is unsupported behavior. From the MSDN "A small set of applications are pinned by default for new installations. Other than these, only the user can pin further applications; programmatic pinning by an application is not permitted."
That goes for unpinning as well. You can read about it here:
https://msdn.microsoft.com/en-us/library/dd378460(VS.85).aspx
Because the mechanism for setting and removing the pinned apps is secret, we cannot support any of the functionality around the pinning process or define the results and outcomes of interactions with Virtualization.
There is no solution or workaround at this time and is recommended to not pin virtualized application shortcuts that are not put there by the applications installer.