There is not an issue with Kodi in this regard. There is an issue with people misunderstanding how it works. People often think the source information has something to do with their database and it does not. The sources are used by the scraper. Once a media item is scanned it is stored in the database as an absolute path. If this absolute path changes then Kodi has a way to fix this without messing with your library. As for the cleanup script it simply looks to make sure the media is there and deletes the entries if they are not valid. In normal use this would only be someone deleting a movie or TV series out of their collection. I do this all the time and it not only works, but it normally runs in less than two minutes on my setup. If it takes forever it is probably because the network device it is checking is no longer there so it has to wait for the network to time out looking for that machine on every entry since there is not a computer there to send back a message that the file does not exist. I believe Kodi sends a message when this happens that you have to agree to for this to even start removing items from a non-existent machine. The quick and easy option here to clean the old source would be to remove the media source from Kodi without editing it and agree to delete all items from that source. Once the source has been edited that doesn’t work as it would be deleting media matching the updated source, not the original one with broken file paths.
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