So, much like snapshots, Linked Clones are not intended to be permanent. One customer had horrible OS performance and log on times after never refreshing desktops over their entire life, a refresh fixed all the performance problems. Another forgot to uninstall VMWare Tools and the VMware Tools\View Agent part of the registry became a dumpster fire when they tried to update the agent.
ThinApp can be a pain but if you need to isolate applications, it is the best thing out there. If you have Horizon Enterprise, you can look into App Volumes. It is much easier and faster performance wise, you will need to use it in conjunction with ThinApp for any applications that require being isolated. If you do not have enterprise and it is too pricey, you can look at LiquidWare Labs ProfileUnity with FlexApp. It is very similar to App Volumes in it's approach.
