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Calibre is primarily a database application, not a file system application - that is what makes it flexible and fast. The database (metadata.db) must be kept in synch with the author and book folder files. I'm not willing to speculate if any of the file synch tools will reliably maintain that synchronism.
A file synch tool certainly wouldn't know what metadata changed in the database - at best all it will know is that the database has a different checksum, size, and modified date.
Why do you want portable on your thumb drive, the normal reason is so that you can use it on public/friends/work computers. In which case most people would regard it their primary instance of calibre. In that case they might use a file sync tool to maintain a mirror copy of the thumbdrive's Calibre Portable directory on a desktop hard drive or in the cloud.
BR
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