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This is probably stating the obvious, but it's ridiculously easy to set a bunch of env vars, and then put yourself outside the context you've set them in. Like logging in as another user who doesn't have it set in the first place, su'ing without the -, or forgetting to export the vars in a script.
Since it's headless, you're remote logging in, and I assume not directly as the user the service is running as.
Does wrapping calibredb in say, a calibredb-wrapper script that does nothing but set and export the vars you need, and runs calibredb work?
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