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Thanks all for your tips!
After some trial & error syncing with syncthing seems to be working (I get no conflicting files up until now). Before I make any change in any Calibre instance I pause all synced Calibre folders. After I do change something in Calibre on one device I close Calibre and then resume syncing on the same device. After syncthing has registerd the change I resume the synced folders on the other devices. The syncthing settings which I use are:
Folder Type: Send & Receive
File Pull Order: Newest First
File Versioning: Trash Can File Versioning
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