You’ll know everything is complete two ways:
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There will be no “Library/Application Support/ Plex Media Server” structure in the “Plex” shared folder. It will all have been moved to “PlexMediaServer/AppData/Plex Media Server”
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The file “Plex/Migration.log” will detail each step of the process and finish with “Cleaning /volume1/Plex”
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Any media you had placed in the Plex shared folder will remain there.
The Plex shared folder is now free for you to use as you deem appropriate.
After migration:
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The user “Plex” is no longer needed.
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You will now need to grant "System Internal User PlexMediaServer permission to read your files (we were forced to change the name)