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Syncing a library via dropbox while it is also being served by a calibre web server is a recipe for data loss. If you want to add books to a remote calibre server instance use calibredb which can connect directly to calibre-server. You can also add books via the web UI of the calibre server directly, and at some point in the future the calibre GUI will be able to connect to a server in some fashion or the other.
Although since you are using debian packages, I have no idea if any of that will work given that they are typically broken and aeons behind mainline calibre releases.
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