when you occur issue "The reference in the deployment does not match the identity defined in the application manifest" in Click once deployment with VS 2008/VS2010. please reference the following steps.
Scope:
Winform or WPF application:
Steps:
1. Create a solution with two Windows Application projects, WinAppA and WinAppB.
2. Set WinAppA as publish project and add a reference to the WinAppB.
3. Open WinAppB properties window.
4. Click Signing tab, sign the ClickOnce manifests.
5. Click Security tab, enable the ClickOnce security settings.