For the sake of completeness for others who may stumble across this thread and were looking to get a completely clean library without affecting the rest of their install…
Via SSH
NOTE: The following is non-reversable. Backup beforehand if you think you may need your old library.
systemctl stop mediacenter
cd ~/.kodi/userdata/Database
rm MyMusic*
rm MyVideos*
rm Textures13.db
rm -r ~/.kodi/userdata/Thumbnails
systemctl start mediacenter