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Just run calibre on the main library on your desktop. Rsync the library to your headless server periodically via cron or similar. If none of the user accounts you create for the server have write permissions, then doing so is mostly safe. I am speaking of the calibre content server here, not calibre-web, I have no idea what semantics calibre-web has.
The only thing you will lose this way is the ability for your users to have persistent annotations made via the in browser viewer. Since those are stored in the db and rsyncing will clobber them.
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