Well, it took some time to respond. Shame on me

After enabling Copy User Data and if everything works fine, should we then disable it?
You're right. Once all the data is copied and everything works, you can disable it. In most cases a single start (maybe some button clicking inside the program for it to try to reach all the data is required) is enough. It's not critical to leave it enabled, but it's the best practice to disable it once you're done.
A second question concerns how to update User Data. Is it a simple matter of enabling this feature or should something more involved be done, for example deleting the appropriate ReHIPS User folder?
Isolated environments have their own settings. So basically they live their own lives. And usually it's not recommended to mix isolated and non-isolated executions of the same program. So no simple way to sync settings besides deleting and recreating isolated environment.