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I mean, how does Syncthing know not to copy a file again if it copied it once and paperless deleted it?
The client on the sender side (the phone) knows it sent the file. It doesn't care if the receiver side changed or deleted it. It sent the file. Its job is done. That's why the mode is called "Send Only".
Meanwhile the client on the receiver side (my NAS) never pushes changes back. It only responds to received sync instructions. That why the mode is called "Receive Only".
It's... all pretty simple. Not sure where the confusion lies?
The phone sync client would have to remember all the files it ever sends, which could be thousands. I've never seen a sync client that works like that, they usually compare the files that are in the source and destination folders. If syncthing can do this that's really interesting.