ThinApp does not support network interface virtualisation. The entire network interface is still handled by the native OS. This includes firewalls, ip addresses and DNS lookups.
So unfortunatly at the moment there is no way to do this. (Sorry, it is one of the features i would like to see as well)
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Theike is right. The problem is that all host name lookups (even those referencing the hosts file) in Windows are done via the "DNS Client" service, which runs outside the virtual environment. Since the DNS Client service doesn't see your virtual hosts file, it gets ignored.