So, I have packages and apps used in TS. Despite reading that apps tend to break I have not seened this behaviour yet. The only weird thing is that as long as I have apps in TS I can't use an uninstall deployment (I always use 2 deployments to every app, one install and one uninstall to two different collections). I Think the reason is because the app have the TS reference as install, which will always win over uninstall. If I disable the app step the will uninstall. I have not tested supersedence, but it will probably not work.
These are the alternatives I've found:
1. Deploy TS to a seperate Collection (direct memebership) rather than all workstations. I will have to put the clients in this Collection every time I want to run the TS and then remove it after so future uninstall deployments work.
2. Disable the apps in TS every time Before an uninstall.
We don't have plenty of uninstalls, only when updating standard apps which will need to be uninstalled before installing the new version.
Anyone having other suggestions?