I want to convert a bunch of FLAC files to OPUS, keeping the folder structure and all metadata (including the cover art). Does anyone know the best way to do that? All the finished scripts I found don't fulfill all of those requirements.

Needs to be something for Linux
@LilaHexe I wrote a Python script for this and mostly works-ish. You could give it a try:
git.tamara-schmitz-devel.de/tschmitz/pymediascripts/src/branch/main/music/musicbatchconverter.py

thumbnail preservation in ffmpeg is uhh not amazing if u want mod it. i don't remember if it works in its current form.
@LilaHexe also beets.io exists. i am not sure if this fits all your requirements
beets: the music geek‘s media organizer

@tammeow wait beets does transcoding?!!
@LilaHexe mhm!