@Insomnic_1 one of the hiccups I’ve noticed in the past when I move media around either from one location to another or like you done Add all of the letter folders && remove the parent folder in the same step that --analyze-deeply seems to want to be done on everything that was moved again.
Look for stuff like Debug — [JobRunner] Job running: FFMPEG_EXTERNAL_LIBS='/var/lib/plexmediaserver/Library/Application\ Support/Plex\ Media\ Server/Codecs/62cc2bc-4226-linux-x86_64/' X_PLEX_TOKEN='xxxxxxxxxxxxxxxxxxxx' '/usr/lib/plexmediaserver/Plex Media Scanner' '--analyze-deeply' '--item' '30526' '--log-file-suffix' ' Deep Analysis' and see if you see this during nightly maintenance. If so its being regenerated and will take some time to complete depending on your content.
I had a thread on this in the past Regeneration of `intro markers` after moving plex media server from one System to Another which was somewhat related.
