Did you change any of the default locations for the Plex data folder or the transcoder path?
(Settings - Server - General - ‘Show Advanced’ - “The path where local application data is stored”
and
Settings - Server - ‘Transcoder’ - “Transcoder temporary directory”) ?
Did you point any of your Plex libraries to the same folder which is used by one of the above settings? Edit your library(s), go to the ‘Add Folders’ tab to find out.