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So it turns out, both problems have to do with the order of signing. You absolutely have to do it in this order:

1.) Build Bootstrapper bundle
2.) (Do not sign the bootstrapper at this stage)
3.) Remove "engine" with: wix burn detach PATH_TO_BUNDLE -engine PATH_TO_EXTRACT_ENGINE_TO
4.) Sign engine (doesn't matter if using signtool, dotnettool sign, local cert or trusted signing/artifact signing)
5.) Add engine back to bundle (creating a new file) with: wix burn reattach PATH_TO_BUNDLE -engine PATH_TO_SIGNED_ENGINE -o PATH_TO_SIGNED_BUNDLE
(where PATH_TO_SIGNED_ENGINE == PATH_TO_EXTRACT_ENGINE_TO).

If you just sign the bootstrapper and not the engine, none of the tools will complain, but t…

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@robmen
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Answer selected by twoelfer
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@twoelfer
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twoelfer Apr 6, 2026
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@robmen
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@twoelfer
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twoelfer Apr 6, 2026
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@twoelfer
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twoelfer Apr 7, 2026
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