Extra files not copied when a convert command is used on import

I’m using filetote and it works perfectly fine when I just import. However, if I need to do a convert (e.g. .wav > .flac) It does not pull any of the extra files. I imagine this is because during the convert it’s moving the .wav files to a temp directory and not the extra files, so to beets. there are no files to be moved at this point. Is there something I’m missing?

  auto: yes
  format: flac
  copy_album_art: yes
  never_convert_lossy_files: yes

This is the relevant command I’m using. I feel like if I could just do the conversion in the import directory first everything would work itself out. Has anyone else faced this issue?

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