PMS on QNAP NAS - deleted my codecs folder - HELP

First of all, you have verbose logging enabled, please disable that.

You also need to move your medias, since they are stored here:
"/share/CACHEDEV1_DATA/.qpkg/MediaSignPlayer/CodexPackExt/share/Shared

See: Qnap faq.....read me first!

Also your naming if off here!
/share/CACHEDEV1_DATA/.qpkg/MediaSignPlayer/CodexPackExt/share/Shared/TV/The Mighty Boosh Season 1-3/The Mighty Boosh Series 1/The Mighty Boosh - 103 - Bollo.avi

If I in above assume, that your show library is pointing towards: /share/CACHEDEV1_DATA/.qpkg/MediaSignPlayer/CodexPackExt/share/Shared/TV
then the show it self is named:
The Mighty Boosh Season 1-3/The Mighty Boosh Series 1/The Mighty Boosh - 103 - Bollo.avi

If so, the show itself should be named as:
The Mighty Boosh (2004) {tmdb-7166}/Season 01/The Mighty Boosh - S01E03 - Bollo.avi

See: https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/

When above is fixed, we can start to look at Codec, but for now found:

Line 5719: Nov 17, 2022 19:18:43.319 [0x7f69dba1bb38] DEBUG - [JobRunner] Job running: FFMPEG_EXTERNAL_LIBS='/share/CACHEDEV1_DATA/.qpkg/PlexMediaServer/Library/Plex\ Media\ Server/Codecs/2427c16-4416-linux-x86_64/' X_PLEX_TOKEN=xxxxxxxxxxxxxxxxxxxx "/share/CACHEDEV1_DATA/.qpkg/PlexMediaServer/Plex Media Scanner" --match --type 2 --log-file-suffix " Matcher" --item 47407

So are you saying that the directory /share/CACHEDEV1_DATA/.qpkg/PlexMediaServer/Library/Plex\ Media\ Server/Codecs is empty?