Input file application.exe missing or invalid: -163

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This is a message you get when BOINC starts up and checks through its client_state.xml file if everything is still hunky-dory. When it finds that it contains a file that you don't have, it'll notify you with this error message.

If you're not running anonymous platform applications, a project reset is in order.
If you are running anonymous platform applications, best check the contents of the app_info.xml file against the applications you have.