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Looking at the Plex API, I would actually much rather rewrite the whole thing to use the API to do this. Seems much safer than directly using the database. Plus you could to with the server running.
per: https://support.plex.tv/articles/repair-a-corrupted-database/
Plex is using a custom version of sqlite, this script should allow for it to be specified, since it won't work anymore.
A possible way to get it working is listed in this stack overflow: https://stackoverflow.com/questions/48865416/how-to-use-the-latest-sqlite3-version-in-python
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