I have now found a way to also deal with fixing updates to server objects not getting synced, which involves a toggleable alteration to the basic delta algorithm which is also backwards compatible with the old one, and with existing Joplin clients. So if #13054 gets merged, it will fix the issue in it's entirety 
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Thanks for your effort on the pull request! IMO a change like this is necessary to make file-based sync work properly with notes with large attachments when using syncthing or similar. Will gladly test this when builds become available
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