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Library scans and picking up added/removed media, kill me. I love kodi, but how such a basic function can be so squirrely I'll never understand. Maybe it's just a quirk with NFS back ends.
I let Radarr and Sonarr handle that (including creating NFO metadata and fanart files), Kodi now only parses/syncs that local data.
This change was a huge improvement for me, though I am using SMB and not NFS. (But I assume NFS would be more robust than SMB.)
Same here regarding *arrs handling the data movement/layout and nfo files. I even have the "Connect" sections for each set to trigger rescans, but it seems especially for files that get replaced by a more optimal version, a duplicate is left over in kodi alongside the new one which only goes away when you try and play it. I tried switching to a dedicated mysql instance for shits and giggles, no effect. Some day I'll actually dig in the logs.