Plex Update Service deletes "LocalAppDataPath" registry key

Which Windows user account are you using to start the Plex server task?
What kind of user account is this?

In which registry user branch did you create the LocalAppDataPath key?

Check the path to the Plex Media Server.exe which is called by the scheduled task. Ensure it is pointing to the 64 bit version of the PMS .exe – i.e. C:\Program Files\Plex\Plex Media Server\Plex Media Server.exe
and NOT C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Server.exe

Have you ever downgraded to an 32bit version of Plex Server?
Ensure that you have only the 64bit version installed.

Consider switching to PMS as a service