Returning to this question, I found another partial solution. It turns out that the wrong protocol dialog does not block javascript execution as a warning.
So, here is how you deal with the backup when you start the application from the Internet:
- Register the setTimeout handler to redirect to the backup page (with the .location.replace window) after, say, 500 ms
- Register an onBlur handler that cancels the timeout
- Open the url with your custom protocol
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