Has anyone had issues with the contents of an isolated storage directory go missing or not update properly after a click once automated deployment?
Go "missing" -- yes. I'm not exactly sure how ClickOnce handles updates but I've seen where a new release would not have the same data directory associated with it (or it wouldn't move the contents forward). I was able to find the old file manually and copy it forward myself when necessary so for the user's application data I required them to specify a destination that they could easily set if the app lost the link to it (which was stored in IsolatedStorage).
If the version of your application changes (I am uncertain exactly which version number it is) then new deployment creates a new folder for storage. There are 2 ways in which isolated storage stores the data:
- Isolation by user and assembly
- Isolation by user, domain and assembly
In both cases, when the assembly changes the directory changes. I do not know what the best way to keep the data between deployments is, but that is the reasoning for it.
I believe you can find your answer on this post - ClickOnce and Isolated Storage.